Evangelion: An Angel's Gambit
by Blades of Chance
Summary: Third Impact seems in motion. Many groups have their plans for the event. Waking up after billions of years the mother of humanity decides to make her own play at stopping the event. Can Shinji, Asuka, and Rei succeed with the task thrust on them by the ancient angel? Or is somethings just destined to happen? Only time will tell as figures manipulate the war behind the scenes.
1. Prologue

**So, yeah I am making another story. I had thought about this one after rewatching the series (and the Rebuild Movies) and I figured why not make one. So after three days, this story came into being.**

 **This story will be more of an "Ultimate Universe" of the franchise. If you don't know tropes it means I would be using things from different continuities (like the manga, Rebuild, etc.).**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Pain was the first conscious feeling that she felt in… ' _How long was I out?'_ The last thing she remembered was a warning system blurring. Something about an impact and then she fell unconscious. ' _Why… why can't I move?!'_ Panic filled her as she managed to open her eyes. ' _I'm still wearing my mask.'_

She saw something happening to her legs. Being cut apart by some weird machines piloted by something. Lilith tried to reach out with her A.T field. The weak field managed to just touch the beings within the machines. If she could her eyes would widen in surprise. It was something made by her. ' _By the pit!'_ This was the worse thing she could wake up to. Her own children ripping her apart for some reason. " _Why are you doing this?!"_

Her attempt to scream with her A.T. field failed on deaf ears. She was too weak and furthermore their own A.T. fields were so weak to pick up anything. All she would succeed in doing would be to scare them. A feeling of desire through her mind at this. She was stuck like this or worse. "So, how goes the extraction process?

Her attention was pulled to two other figures walking up to the pool of her blood. Reaching out with her A.T. field she managed to catch enough of their language to at least understand what they were talking about. Reaching into the older of the group she managed to see flashes of what he knew. The first was something called Second Impact, and Adam. Lilith if she could, would be wide-eyed at the fact another Seed had landed on the world. A seed that they awoke and nearly destroyed the world!

' _By the pit, don't they know the threat that they unleashed on themselves!?'_ This wasn't supposed to even happen. They each were sent out into the void of space for different targets. Each had a target that should have been light years from each other. Even on the off chance that it did happen, they had the means to ensure that both sides didn't kill each other. That was no longer an option. ' _I have to be free it's the only chance my children have!'_

Lilith tried to link with her Longinus. Whatever was happening to her she could break it with it. The progenitor to humanity felt nothing coming to her. The all-purpose tool wasn't flying to her hands. It was destroyed by the impact. Panic consumed her before she pulled herself together. Perhaps her children had figured it out themselves? What she saw caused more questions. ' _They are using me to create things to fight Adam's spawn?'_

It sounded so wrong and yet if this was the only option that they had then what could be done? If they did manage to find her Seed-ship and her then it was possible that they could pull it off. The ancient being was content on this. If the greater good demanded it then so be it. At least her children would have a fighting chance against Adam's.

* * *

The next few weeks after the harvest Lilith just spent trying to extend her A.T. field. Gathering her strength she was able to see through the eyes of those working in the slowly being constructed facility. From what she had learned caused her pause. They didn't seem to locate anything from her seed-ship but her. At least from what they had seen. Though they seemed to have an understanding of some of the theoretical framework for many things that she knew about.

What she did see was them working on something. The designs for what could be described as a mockery of what she once was. A tool to fight the Angels as they called them. For a time Lilith while disgusted at what they were doing was content with the thought of the greater good. At least until she discovered the truth. The woman Yui, obvious to it, had explained what they were actually planning.

Lilith couldn't believe how badly they misunderstood everything. First, they thought the Dead Sea Scrolls, a corrupted warning made by her ships computers, was a means to a path to ascension. A means to either turn them into a hive mind or something. ' _What next are they planning to fuse me with Adam?'_

Her bitter thoughts aside Lilith was pissed at all of this. She had thought it was an accident that they had to awaken Adam. Nope, it turned out they were crazy enough to actually do it. That just brought them to how they had hoped to accomplish everything. ' _A hybrid?'_

Yui was getting to work on using her makeup and Lilith's in hope of creating a means to control Lilith. As she had planned her husband would find them active them and begin a means to set in motion both a plan to get her back and SEELE's while she got to complete her own plan. Speaking of Yui her plan was to become a god. ' _Is everyone here crazy?'_

As for their plan to control her, it was terrifying. They were going to rip out a part of her soul and stuff it into the clone. Lilith knew that such a forceful thing could render the newborn soul blank. A doll as Yui was hoping. Rage built up into Lilith at this. Her gaze soon caught sight through her A.T. field of Yui child. ' _They are planning for him and two other children to pilot their abominations.'_ An idea crossed the mind of the ancient being. A fiendish and dare she say it mischievous. ' _Let's see how they feel if I give the keys to them instead?'_

It was rather complex yet so simple in the end. Using their own plans against one another. The first thing to do was to find a person to influence. A few caught her eye but the one that she had planned was the current physician. With some taxing actions on her part, Lilith was able to gain control of her. When Yui's child came for a check-up Lilith now in control decided to do a little change in his check-up.

* * *

"Now, before you go I have something for you." The possessed physician walked over to a syringe with water and something else floating inside of it. As she held onto it Lilith let out a low pained groan.

Seriously if this was the pain with only a tiny bit then she was dreading what was to come later. Turning back Lilith in her bored body looked at the little boy. It was hard to think that he had no idea the kind of insanity he was going to be thrust into. For a moment Lilith hesitated to what she was going to do. Mentally reinforcing herself she looked at him. "Give me your arm."

Shinji looked a the syringe in her hand for a moment before handing her his arm. Taking it she injected the fluid into him. When she was done she tapped his shoulder. His body shivered for a second after this. "Thank you now how about I get you something for being a good boy?"

Lilith turned around as she looked through the treats the doctor had for him. The syringe contained a tiny bit of her angelic DNA. Pointless on its own but with the near insignificant bit of her soul she had managed to rip off and left into him that would change.

Already his soul was assimilating it into his own. The change in his A.T. field would cause the small DNA proteins to be copied and assimilated it as well. The effect would alter his DNA and physiology but in the end, he would become something of a hybrid. Nephilim was the name for it. "Here we are," She handed the young child a candy. "You know your future will be rather interesting."

* * *

Altering the genetic structure of one of the clones was a huge choir as she tried into the room storing the clones. Once she did she looked over the genetic makeup of each of them. A glare formed on her face due to how many errors and problems they each had. It was like they were made to be unstable. ' _Who am I kidding, of course, they were made unstable.'_

It was easier to control them if they were biologically unstable. She looked at each of the clones and their lists. "Rei?"

If she recalled Rei was one of two names that Yui was planning to call her child if Shinji had turned out to be a girl. Lilith looking over the genetic code hardened her gaze. These clones had enough genetic material to look like her physically. The rest was altered due to wild mutation or was from Lilith's. If anything she was more Rei mother then Yui. ' _You know I never had a child before.'_

True humanity was her children but that was in a figurative sense. Lilith got to work stabilizing the genome of the clones. She hit into a snag one it turned out that it would take a lot longer then she had liked. At best she could get only one of them to be fixed up. ' _Rei I is too genetically damaged though Rei II was able to be fixed.'_

Fixing the genes was rather difficult to do. The vast patchwork left several unstable genes. Nevermind the problem of Yui walking in on her. As luck would have it she was finished as the still-developing soulless clone was finished. "There we go all better now," She erased the records of what she did from the computers. With the way security was in this place, she had to make sure there was no trace to be found. Walking out of the room Lilith caught one last sight of the clones. ' _You're a true hybrid.'_

* * *

In hindsight, she should have looked up just how far they were to Germany from her home/prison. Still, her goal to subvert the plans for their first three children. Pushing back her pain she walked into the German branch with a single goal being repeated in her mind. She looked around as she pulled up the map.

' _Let's see I should go down here…'_ She stopped as she saw Asuka sitting on one of the benches. That made things a lot easier though she had an idea as to why.

Her mother was insane. Driven so due to her broken soul. SEELE was hoping that she would eventually kill herself so they can stuff her into the Evangelion they planned for her to pilot. "Asuka Langley Soryu?"

She looked up at her. The girl seemed to give her a questioning look before she noticed her name tag. As she spoke Lilith was grateful for her A.T. field being able to translate for her. "Are you the new doctor for mom?"

The ancient being felt rather bad about what was going on with her mother. However, She knew she couldn't fix what had happened. That could only cause more problems if she tried. "No, I am actually here to serve as the new physician," Taking out the clipboard that she had in order to play the part. "I was actually looking for you for your schedule check-up."

Asuka didn't seem all that happy with that. Lilith didn't know why and she didn't have much in the way of time to figure it out. Asus still went along with some minor fuss. Taking out the syringe she had packed she turned to her. "Now please give me your arm," Asuka extended her arm too her as Lilith injected the fluid into her. "Done so what do you say to a treat?"

Lilith placed her hand on her shoulder as she passed the sliver of the soul that she had prepared for her. Asuka felt a jolt go through her spine. She chose to ignore this. "No thanks."

* * *

Lilith groaned as she returned to her body the strain being almost too much for her. She took the time to let herself recuperate. Unaware to her as she was regaining her strength that now was the time that Yui choose to be absorbed into Eva-01. Those setting off events leading to his father abandoning him and learning all that Yui was working on. A plan formed in his mind. One which while ironically following both SEELE and his late wife's at first glance would have his own goals, not in others interests.

Lilith after regaining her strength in the last week knew that soon they were going to extract her part of her soul. They had managed to jerry-rig a device to do so. Lilith's A.T. field burned unto her flesh as she reached into herself. Unlike with the other two, this fragment she was about to break off was much larger. Lilith nearly fainted but in the end, she succeeded and ripped out a fresh blank angel soul from her own. Nearly blank as Lilith managed to edge something into it. The names of the other two and her mother.

As she felt this new fragment leave her Lilith felt herself fall back into a dream-like state. If she could she would have a smile on her face. Her actions had hopefully done what was needed to prevent this insane plan from coming into being. With her eyes closed, she entered into unconsciousness as her dreams were nothing but a mix of colors.

Nothing changed until she was vaguely aware of something. A minor touch on her A.T. field. An image formed within her dreams. It was close to her, close enough that in her half-conscious state that she could reach out to it. "Who are you?"

Lilith paused as she realized ho this was. It was the soul she had created from her own. The first child or Rei as the humans had called her. "My name is Lilith."

"What are you?" The question was one that had given Lilith pause. She didn't expect this to happen but it seemed that she was able to communicate with Rei even though her soul should be diverging from the piece of her own.

After thinking about it for a moment she responded to the question. "I am your mother."

* * *

 **So, to keep track we have SEELE, Yui, Gendo, and Lilith all having their own plans for the war with the Angels. Each one of them having goals that run counter to each other. Oh, and I picked a more unfavorable interruption of Yui motives because I figured if she is the daughter of someone in SEELE then she should be more like them in the thought process. That and because it's rather common practice (from what I have seen) for her to be heroic.**

 **As for what Lilith's actions did to the first three children. Well, first off the effects of the DNA injects warps each of their genes (both human and angel) so there no genetic similarities. In case you were thinking about it.**

 **I will be seeing all next chapter.**


	2. Chapter 1

**Well, if you are here in America then happy thanksgiving. I figured I might as well post a new chapter for the day. Yeah, I tend to write the chapters with four thousand or more words so I apologize if it seems rather small. Also, this chapter can be considered a set up before I get into the story proper. Consider it the set up for the status quo moving forward.**

 **Now as I usually do I like to thank the reviewers. So thank you** **rjcelona, S-01, Scattershot98, and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix (?), Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Ever since her rebirth from being killed Rei had felt a presence in the back of her mind. The blue haired girl couldn't explain it at first but soon she had found out why. That presence was the A.T. field of Lilith which she could feel thanks to her close connection to her. Naturally, this was a surprise to learn.

The bigger surprise was that she should actually have Lilith's soul so being able to communicate with her shouldn't be possible. Keeping this revelation to herself Rei soon learned why from her mother. Lilith had ripped out a part of her own soul in order to give them something to put within the clones. ' _So, that means I am not what Commander Ikari wants me to be.'_

To the outside observer, it appeared that she was all by herself sitting with just her thoughts. Really though this wasn't the case as someone was listening to her. " _Your Commander kind of lied to you about a lot you know,"_ Lilith while still too weak to talk for prolong periods felt that this was extremely important. As such she powered through the pain. " _For instance, it wasn't him who created your clones but, his wife who I might add didn't actually love him anymore at the time she disappeared."_

Any normal person would laugh. Especially if they knew Gendo whole plans. Lilith had an idea of it having just touched his soul once before during this time. The man was madly in love and wanted to be with his wife again. ' _Then what is my purpose then?'_

Rei should tell the commander about this but she wasn't so sure. " _The plans of both the Commander and SEELE are based on misinformation and thanks to them Adam's spawn will be looking for me and him,"_ Lilith was certain that Adam wasn't dead despite blowing up. If he was alive then naturally his children would seek him out and a means to wipe out her own. " _I had fixed the patchwork of a body you currently inhabit making it actually healthy and eventually able to allow you to use your own abilities."_

That was true as she didn't feel any pain from supposed defects. In fact, her LCL treatments didn't seem to do anything for her despite it being done to help heal her ailments. Ailments that were thanks to her being a clone hybrid. Lilith's action had done away with it even allowing her body to start developing things her previous body lacked. " _I know what they are hoping to achieve and the disaster that it would become, their Human_ _Instrumentality Project_ _, as such I am hoping that you are the other two can stop it by breaking control to you three."_

Rei looked up as her body showed a physical reaction to what was going on. There were two others like her? ' _What do you mean?'_

" _The second and third children,"_ Rei understood what she was talking about. There were two other children who could pilot the Eva's one of which she knew was in Germany and the other being Vendor's sons. " _I managed, with a lot of effort, to turn them both into beings like you in order to make sure that there is no way for Third Impact to happen."_

Continuing to look in front of her Rei processed this. ' _What about the angels that we are supposed to be fighting?"_

" _They will still have to be defeated,"_ SEELE very much had a limited understanding of the relationship between her and Adam. They did know that the two of them were of different seeds but they didn't quite understand it. " _Both me and Adam represent different ideals that the First Ancestral Race once fought over and we weren't supposed to end up landing on the same world together."_

The progenitor of humanity believed that the only reason Adam's spawn will be coming to her is that they will mistake her for him. If they manage to actually find and merge with the real Adam then they would be in trouble. While it was likely that his seed-ship was destroyed they would still be able to improvise a means to wipe out her children in order to inherit the planet. Their version of Third Impact was nothing short of the extinction and terraforming of the world to their ends. " _The war will have to be fought and each one of them has to be killed."_

The blue haired girl gave her a nod. She had to cut the conversation short as Gendo walked in. Today they were hoping for her to do her first harmonic test with Eva-0. The angels were for a few years from now but that didn't change the fact that NERV was to be ready for them. Several minutes later Rei was in her plug suit as she stood looking at the Eva that she was to pilot. Its metal coverings hid the fact it was actually made from Angel flesh. A fact, she remembered from her past clone.

Once she was inside she listened to the voice on the other side. The voice of Doctor Ritsuko Akagi the chief scientist of NERV. "Alright, we going to flood the LCL," Rei didn't react as the fluid filled the air around her. She knew better than anyone that it was breathable. "Alright, now let's get started."

As the test started Rei synchronization rate increased steadily. Inside it, however, she could felt vaguely aware of think. As soon as the sync started to pick up Rei's eyes shot out as she felt something around her. An unknown sensation started to boil up within her reacting to something that she didn't understand.

Outside looking over the computers Ritsuko started to notice the sudden anomalies. The scenes were going haywire as Eva-0 was starting to twitch and thrash around. Gendo looked at the actions in front of him before turning to Ritsuko. "What is going on?"

"I don't know nothing is responding to anything do!" Ritsuko had tried the emergency ejection but nothing was coming of it. "I'm cutting the power!"

Deep inside Eva-0 Rei opened her eyes as her suit started to tear apart. Behind her two wings shootout two pale white, opaque wings that looked almost like extensions of her own body before a the Rei let out a scream. Eva-0 stopped before turning off whatever happened that caused this ceasing as everyone moved into to remove a now unconscious Rei.

* * *

Lilith wasn't surprised when she felt Rei's awakening. What surprised her though was the fact that it had happened thanks to the harmonic test with Eva-0. The ancient being knew that it was made with Adam's flesh and forced in a soul from someone else. It was possible that the environment of combined with the synchronization it reacted with her physiology and awakened it. ' _I guess she will need training in use it especially for the war ahead.'_

This made her wonder about the second child and third child. Unlike Rei, their bodies were still developing into what they are to become. Lilith wondered if the same stimuli would trigger their own awaken or would it be something else? Stopping her train of thought she had to see if the effects of Rei's awakening had caused them any trouble.

Reaching out with her weakened A.T. field she did a sweep on the NERV headquarters. The scientists who deal with the Eva were looking into fixing any technical issues thinking something might have been off. Gendo the man Lilith was most concern about was taking this as a random event though he was going to keep his eye on it. ' _At least she didn't sprout her wings in front of them.'_

When they found Rei she was unconscious with her plug suit in shreds. Right now she was resting in the infirmary though if Lilith could tell it was more an aftershock from the sudden awakening. Her A.T. field had a low yet noticeable hum to it though it was hiding its true strength. Training her was going to be a huge hassle as she was certain that there was no place that Gendo wasn't going to monitor.

' _Perhaps we could try theoretical training,'_ Lilith retracted her A.T. field as she felt herself grow tired. She has used up a lot of her strength and needed to rest for a moment.

* * *

Asuka spat out the toothpaste in her mouth as she looked at herself in the mirror. Staring back at her was her blue eyes which at a distance would seem normal to anyone. However, close up one would see that her pupils were oval shaped like that of a cat. The other difference was within her mouth. Her top pair of canines had lengthened over the years looking more like fangs than anything else, while the rest of her teeth seemed to sharpen as well.

These changes always stared back at her whenever she looked in the mirror. At first, they weren't all that noticeable and when they started to become so the personnel just chalked it up to side effects of Eva piloting. A few of them even commented that it made her look threatening.

For Asuka, these changes were barely an afterthought. The one pain was how sharp her 'fangs' and teeth were. She had actually managed to bite through any eating utensil she was given. Even metal forks and spoons were quick to break under them. It also made brushing them an utter hassle as they would cut off parts of the bristles if she wasn't careful.

Still, there were several benefits to them that she wasn't complaining. Though her other habits were things that the local doctors kept her monitored over after her first few tests. Thinking about it always allowed her. ' _I mean so what if I was drinking the LCL fluid it was tasty and it's not like it was poison!'_

Another thing that brought confusion was her inability to properly inject cooked meat. Whenever she did she had to fight the urge to throw up as her stomach couldn't take it. Raw meat was a completely different story as she not only could eat it without any side effects but she actually preferred it. The usual health issues were surprisingly missing. She had a mental chuckle at this. ' _Guess I'm made of tougher stuff.'_

She walked out and down the halls of NERVes German branch as she caught a few of the doctors having a conversation. "I am telling you this is all strange that she started developing like this are we sure we don't have another pilot for reference?"

"I don't believe so," The other doctor crossed her arms. NERV was disorganized at the best of times. At the worse, each branch was known to fight among itself. "Even then do you actually think they would hear their findings with us?"

Asuka crossed her arms as she looked at the two of them. It annoyed her that they were still caught up about her weird changes. "You know I can hear you!" The two of them were using English to talk to each other but Asuka understood what they were saying perfectly enough. " _Verdammt_ , I get it already I act and look different!"

She didn't have time for this. It seemed like her changes are all that they talked about. So what they were the result of her piloting the Eva Unit? Asuka had made her choice long ago to continue even when they thought the effects were temporary. ' _Honestly, it's not like any of this matters I'm not going to sport an extra limb or anything.'_

The two doctors were left there as they watched her walk away. They both turned to each other as they looked at each other. Truth be told several things about her was starting to seem frightening to them. Besides the physical changes that could be seen it had appeared that she gained a degree of super strength. Finally, the last medical scan had picked up some kind of growth within her body. At first, everyone assumed cancer but that proved to be false when they tried looking for the signs.

She had _grown_ a whole new organ. A completely new organ that seemingly served literally no purpose as far as they could tell. That didn't mean it wasn't vestigial or anything. By all accounts it could be doing _something_ it's just they had no idea. "You know I'm actually scared she might try to bite out heads off," The female of the two paused at this. "And I mean that literally."

The other doctor turned to her with a raised eyebrow. "You are acting like she's some kind of monster."

"You don't think she is?"

"... No comment."

* * *

Shinji did not have the best of time after his mother died. His father abandoned him at a train station to be raised by his godparent. An old associate of his dad. A year later he noticed a change. His eyes had, something much to his confusion and that of the local doctors, developed Heterochromia. What else was neither of them were his old eye color. His right eye was a bright yellow while his left was a bright purple.

This didn't go unnoticed to the bullies at the school that he went too. This only got worse when his hair changed as well. No matter how he cut it the tips of it had turned into a bright grey color. They had spread a rumor that he had bleached it to look like even more of a freak.

The sound of the bell pulled him out of his thoughts as class was ending. Shinji picked up his books as everyone started to talk to each other about what they were hoping to do now that school was done. A few were talking about the possibility of heading off to play games, others to watch the latest movie, or just getting together. As Shinji walked out of the room he caught sight of the bullies who loved to bully him. He turned away hoping that they hadn't seen him. "Hey, Weird-eyes where do you think you are going?!"

Shinji stopped as he knew it was rather pointless to run. He had already tried and all that did was make it worse when they caught up to him. He turned to them as the stared at him with an intimidating look. "L-look I d-don't want a-any trouble."

A round of laughter escaped them at this. The leader of the trio placed his hand on his shoulder. "Really do does this mean that you wouldn't mind if we keep this then?"

One of the other two pulled out from their bag something that Shinji recognized. It was the bow to his mother's cello. Her cello was the only thing he had that belonged to her and he made sure to take care of it and everything that came with it. "H-how did you get th-that!?"

The shock and worry on his face were just what they had wanted to see. "We got it from your bag the other day figured it must have fallen in when you weren't looking," The one who held it in his hands pointed it at him. "I have to say this doesn't look like an actual bow how about we fix it for you?"

Shinji watched as the strong one of the group was handed the bow and before Shinji's very eyes broke it over his knee. The slippers of wood falling on the ground as Shinji looked at it his eyes fell on the now ruined piece of his mother's possession as they tossed it to the ground. "There much better don't you think Weird-eye?"

Shinji's mind looked on almost shutting down at this. For years he had put up with this. He had been bullied by them but never once had something like this happened. They had destroyed something his mother once owned. After a few seconds, he felt something snap in his mind. Before the knew it Shinji grabbed their leader and before everyone threw him into the lockers. Shock gripped them as they saw the dent the force of the impact had caused while Shinji looked over the bully leader.

No one moved as they just stared at him. The bully he threw into the lockers wasn't getting up as his body twitched in pain before them. As soon as he realized what he did Shinji froze in horror. ' _What just came over me?'_

Everyone who had seen this looked at him with fear. The remaining two bullies now cowered in fear at the act they had just witnessed him do to their friend. A few of the onlookers started to whisper to themselves. Shinji looked at his arms horrified at all of this. Finally, he couldn't take it and just ran out of the building.

* * *

Gendo sat in his office as he looked over everything. It was a year until the first of the Angels was destined to arrive. To years ago Rei had her incident with Eva-0 and since then they hadn't had another issue like the one from before. Rei was still making slow progress with her synchronization. After some thought, he had decided to let her wander off outside of the base and even was filling things for her to stay at her own place within the city. Under watch, of course, though he would allow her the privacy of her apartment.

Pulling out the reports he looked at the other things with his plan. His son Shinji was something he had put off for a while though with any luck things should turn out as he had hoped. "Did he start using contacts and hair dye?"

The image of his son's current appearance wasn't as he had pictured in his mind. Though his personality profile was, with a minor incident at his former school, as he had wanted it. ' _Whatever weird quirks he picked up aside it seems that the scenario will play out as I hope.'_

Placing it on the desk he looked at the report that the German branch gave him about their pilot. He suspected that a lot of it was hidden as was expected but it wasn't enough to know that everything was still as planned. ' _I will just have to request that they transfer over then.'_

Getting up from his desk he decided to take a walk across the headquarters. His first stop was to look at the Eva Units. More precisely he stopped to look the one housing the soul of his wife. It was fortunate that he had found all that she had been working on just after the incident. Now, thanks to SEELE he had the means to reunite with her.

Unknown to him someone was watching this. Rei looked at the commander almost feeling pity. The man had no idea how messed up Yui actually was due to her upbringing under SEELE. Lilith even dropped that by now whatever vestiges of a bond she once had with him was effectively gone on the part of her. Rei looked at the Eva-Unit herself as she thought about her relationship with the woman.

Yui was the one who had a huge hand in creating her body. Even using her DNA, and despite the alterations that came about due to Lilith's own, she had made sure she still looked like her. Rei could understand if someone thought that because of this that Yui was her mother or at least a parent. Knowing what she did, about how she had made her clones to fail and break apart, how her original intent was to be used as a cage for Lilith's soul, made her dismiss it.

If anyone was a parent to her it was the thing in the basement. The being who Gendo believed Rei housed the soul of. Gendo turned around and left without a word as Rei knew that he was probably going down below to talk with the crucified Lilith. A ritual that he did every few months.

* * *

Gendo stood looking at the crucified body of Lilith. Out of all the places in NERV, this one was ironically the most secure from eavesdropping from SEELE. Lilith was indisposed and seemly lifeless. As far as he knew he had Lilith walking around in the body of the clone that he had under his control.

"It's almost time for the Angels to come and with it, I only have to wait a year or two at most to be with Yui again," Gendo spoke to the giant in front of him almost like he was talking to someone.

The thing is while he was unknowingly doing so said someone couldn't speak back. Even then Lilith suspected that his reasons for talking to her was due to his declining mental health. Despite being an immediate threat should he ever find out about the truth Lilith couldn't help but pity him. ' _You have no idea what has become of her and if you did I would suspect it would either crush you or doom us all.'_

Gendo turned around placing his hand on his head as he rubbed his temples. "I just know my son will become such an annoyance to deal with when I call him in," Nevermind he will have to at some point get the second child to come to Tokyo-3. He couldn't have a wild card like that. "Still, hopefully, he'll be willing to help even if I have to force him too."

Unknown to him Lilith decided to take a look at what he had meant by that. If she could she would crush him with hands in a fit of motherly rage. He was going to purposely sabotage Rei training just before the day arrives in order to play on his son's feelings. ' _Oh, you heartless son of a bitch I take back any pity I ever had for you!'_

It was worse when she knew that Rei had to mentally suppress her ability to regenerate just to not arouse suspicion. His whole idea for manipulating his son was going to put her in needless pain. Gendo unaware of the killing intend coming off the rather enraged Lilith just went back to talking to himself. "I do wonder though if you are even aware of what I am telling you?" He adjusted his glasses at this. "Rei has shown no surprise or suspicious so I guess it's true that you're just a hollow shell."

' _Oh, I am aware of what you are telling me and so will be my daughter,'_ Rei was good at not showing emotion. A fact which both helped her avoid suspicion but also scared Lilith quite a bit. Despite the awakening of her nature, Rei's soul was still so blank. ' _You know it's actually a good thing that you abandoned your son I'm certain he would be a budding sociopath if he had you as a role model!'_

As much as she would enjoy ripping him apart, and she was _really_ starting to enjoy the thoughts of what she could do to him, he was needed. Fighting Adams spawn would be too much of a problem without the Evas and if they did find Adam then everything will die. Curse, SEELE and their need to poke at things that they shouldn't. "Well, It was nice talking to you Lilith and sorry for cutting this short but I have to get in contact with the committee."

He turned away to leave Lilith to the fate that he thought she was in. The ancient entity didn't react at all. No, she just saved everything he said for later. Both for Rei and hopefully for the other two children when the time comes.

* * *

Shinji looked around the strange dark and almost mist covered area. Confusion was in his face as he looked for any sign of why he was here and what was going on. A sound caught his attention as he looked around frantically for the source. Out of the darkness, he saw a pair an of glowing wings giving some illumination to the mist.

Shinji turned to it as an out like of something stared as him. Two glowing eyes stared back at him. One yellow and the other purple like his own. The creature they belonged too seemed to stare back into his own eyes before he got a look at the thing as it started to rise above him. His eyes widened as he looked at the gigantic creature before him. It opened its mouth and lunged right at him.

Shinji awoke with a fright as he shot up from his bed taking in deep breaths. As he slowly calmed himself down. His mind told him that it was just a dream and yet something about it felt so real. His mind replied the events over and over again as he felt a familiarity to the creature. "Was that me?"

It was the first question to enter his mind. For a second he dismissed it as utter nonsense yet, when he did he felt like he was lying to himself. ' _No, none of this means anything it's just a dream.'_

* * *

 **As we begin our story we'll have Rei already awakened and having to hide it. I also went with giving both Shinji and Asuka different mutation then just copying how hybrids usually looked in other fanfics I tend to have read. Oh, and what was Shinji dreaming about near the end? Well, it would be spoilers. Though I can confirm that each of the children have to hit a certain sync rate with their Eva's if they want to awaken their nature (though there are possibly other ways and Eva piloting is the first I revealed). Just don't expect the next to awaken next chapter or anything like that alright.**

 **Cya all next chapter.**


	3. Chapter 2

**Hello again everyone. You know I'm actually surprised by how quickly I was able to get this out. Made sure to give it a twice over to fix it up. Anyways, you can say this chapter marks the story in full.**

 **Thank you** **S-01, Scattershot98, and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix (?), Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Shinji waited for his call to go through. A small part of him was hoping that maybe his dad would answer. He got his answer when the phone just fell to an automatic answer. Talking about the city being in a state of emergency. Tokyo-3 had plenty of these drills dye to being a fortress city. "You're here."

He turned to the source of the voice. As soon as he did he was met with a girl with ice blue hair and red eyes. When he blinked in surprise she was gone. ' _Wait, was someone just standing there?'_ After a few seconds, he just chalked it up to his mind playing tricks on him. As he did an image flashed in his mind of the giant with glowing wings and eyes colored like his. ' _It's just like…'_

Shinji shook his head at this. He hadn't thought about that in over a year and yet it still lingered within his mind. Doing as he had always done he pushed it to the back of his mind. He stood out on the sidewalk as he pulled out an envelope that was sent a little after his father requested him to come to Tokyo-3. It was all his father believed was needed for him according to his caretaker. Apparently, he was being picked up by someone named Misato Katsuragi. ' _What the.'_ He pulled out a picture of her. "Well, at least I know who is coming to get…"

He was caught off guard by the sudden sounds of artillery fire and the sirens. Shinji turned around and looked wide-eyed as he saw the reflection of some giant creature in one of the skyscraper building windows. As soon as he laid eyes on it an image flashed of that giant from his dream yet again. Shinji shocked his head as he pulled himself out of it.

He turned to run before a car ended up almost running into him. Jumping out of the way it came to a stop as the door to the passer side opened up. In the driver's seat was the person from the picture Misato. "Sorry, about that but you have to come with me!"

* * *

In the NERV headquarters, Gendo watched as the military went on and continued the futile attempt at firing at the Angel. He knew it was no secret that the higher-ups in the military of both the UN and the various governments had some idea about what was actually going on. Despite SEELE efforts rumors about what had actually happened during Second Impact persisted. While none of the UN forces knew actually why the Angels were attacking they still demanded to try to take it out. ' _Foolish effort.'_

One of the U.N. commanders slammed his hand on to the console like this. They had thought that Gendo was only kidding when he said they were incapable of stopping the Angel. Watching it just ignore or casually destroy anything firing at it was starting to prove him right. "Fire the N2 bomb at it right now!"

Gendo continued to watch as a small smirk formed on his face. They were clearly starting to see how outmatched they were in this. The jets scrambled and the military forces firing started to retreat as the missile carrying one of the greatest weapons on the modern world was launched. The Angel barely registered that the missile was coming at it before it exploded tarring apart the surrounding area from the shockwave of the blast. For a moment a smile was on their faces at this. Then the dust and dirt cleared from the video feed as the Angel was still standing. "DAMN IT!"

The report of what they had done came in. The Angel was injured from the blast and while it had stopped to regenerate its A.T. Field it seemed had flared up again. Furthermore, much of the equipment had been destroyed by the shockwave of the blast. Gendo waited a few moments to let the cost of their defeat sink into their minds before he spoke. "Gentlemen I believe that this show has proven my point."

The U.N. commanders let out a sigh of defeat. "Very well then we'll let NERV take their chance at it."

As the three of them walked out Gendo looked on at the image feed. It had been fifteen years and now everything was beginning to go as planned. "Sir I must remind you that our pilot is in no condition to enter into battle."

Gendo turned to his old colleague and the closest thing he had to a confidante. Kozo Fuyutsuki the Sub-commander of NERV and one of the few who knew the full truth of the Angels. Of course, that did not mean that he knew everything. Gendo turned back to the screen as he looked at the Angel. "Misato should be bringing us a spare as we speak."

"A spare?" It took the sub-commander a few moments to realize who he was talking about. "Oh, you mean your son correct?"

Gendo turned to him for a second before giving him a slow nod. Everything should be as he had hoped with him. All he needed was to get Rei for the extra push. "The very same he is the third child."

* * *

When his father had called for him to come to Toyko-3 he did not expect for him to get pick and caught in a war zone. Yet, here he was and was now reading over the document of everything that NERV was and the Angel threat. ' _Second Impact was caused by one of those things?'_

Suddenly Shinji felt something. It wasn't in anyway he could describe but he could just feel like something was here with him. It was like it was watching him and yet Shinji couldn't place his finger on why he was feeling this. He was pulled out of his thoughts as his eyes caught sight of the giant robot before him. He spoke in a low tone at this. "What has my father been working on?"

"Misato I see you made it back with my son." Gendo stood walking into the room. As his eyes locked with his son. He hadn't seen him in nearly eleven years.

As for Shinji seeing his father brought up so many repressed feelings. A part of him wanted to yell at him for just abandoning him at a train station all those years ago. Another part wanted to know why he did that when he needed him. In the end, he didn't act on either feeling. "W-why did you c-call for me after all these y-years?"

Gendo looked at his son right in the eyes. "I need you to pilot Eva-1."

This only brought confusion on Shinji face. After a second of thought, he turned to the giant robot as he realized that his dad wanted him to pilot it. He knew he should have felt betrayed but somehow he just accepted that his father didn't care. "You only called me in to pilot a giant robot?"

"The Evangelion is not just a simple giant robot it's the peak of biomechanical engineering," Walking up to the group was Ritsuko who looked at Misato. "You know I almost thought you had gotten lost again."

Misato rolled her eyes at that remark. So, what if she had gotten lost a few times. NERV was almost like a maze unless you had a map in your hands. Even then Misato had gotten lost a few times. "Come on Ritz I'm not that hopeless with directions."

While the both of them talked Gendo looked at his son his emotions hidden under his facade. Already, he can tell that he was going to have to give him the incentive to pilot the Eva. ' _Can't play my hand in one go.'_ Adjusting his glasses Gendo spoke to his son with a calm tone. "Yes, I called you to pilot the Eva because you are the only one who can do so."

For a moment Shinji wanted to pretend that he could feel happiness at this. After having never seen him for more than a decade and never once giving a damn about him he knew that this wasn't born out of genuine care. Shinji held his head down as he felt anger swell within him. "Y-you bastard," Shinji tried to calm himself as memories of when he lashed out in anger replayed in his mind. "Why can't you get someone else to do it?!"

Nothing happened for a moment as Gendo looked at him. A lot of suppressed anger and issues had for a braid moment had broken through and revealed themselves to the Commander. He could see why Shinji reacted the way he did before. If Gendo could break his facade he would have smirked at this. ' _He is just the right about of unstable.'_ Gendo gave a look of disappointment at this. "Very well then Ritsuko please bring in Rei."

Ritsuko looked at him for a moment hesitant before giving a small nod. She turned around and motioned for the workers to bring her. Shinji's eyes widened in surprise as he saw her. The girl that appeared before him for a moment in his mind. ' _S-she's real,'_ For a moment he was lost in thought as an image of her with two wings appeared in his mind over her image. She looked so beautiful to him. When this image passed he realized just how injured she was. ' _T-they are going to make her pilot that thing in her condition?!'_

Gendo caught sight of his expression as he mentally smirked. Shinji had no idea that Rei life was unimportant given how many clones they had in the basement. In the end, she was nothing and could be replaced. "Rei I need you to pilot the Eva the spare is useless!"

Rei opened her eyes and looked at Shinji. She had sensed him enter the city and reached out to him. Making contact with her fellow Nephilim. In a brief moment, she felt how broken he was on the inside. Even with this, he had a kind heart and a desire to do what was right. He wasn't anything like his parents. As she looked at him she reached again with her A.T. field. She had felt it when she had the short contact. Shinji was mentally denying what he had become. Pulling back she turned to the Commander and spoke weakly. "Yes, sir."

Rei was about to pull herself out with her broken body when Shinji looking at this couldn't take it. He knew his father was trying to manipulate him but having someone in Rei's condition pilot a giant robot against that thing out there. "Stop!" Shinji looked at his father in the eyes. "I'll pilot the Eva."

' _Checkmate my son.'_ Everything went as he had planned. He turned back to Misato who was looking at him with a look of disbelief at his actions. "Misato gets my son suited up and Ritsuko have Eva-1 ready for launch."

Rei looked at Shinji as she was moved out of the area and headed back to the medical ward. She reached out to him again touching his dormant A.T. field with her own yet again. It was brief as she had only one thing she needed to tell him. " _You need to know what you are."_

Shinji looked in the direction of the retreating Rei and her medical bed. He stared for almost a full second before he was pulled out of his trance by Misato. This wasn't the time to think about what had just happened. He had a giant robot to pilot and an Angel to destroy. ' _This is going suck.'_

* * *

Lilith awoke as she felt the presence of one of Adams spawn nearby. She reached out to Rei wondering what was going on. " _Rei what is going on?"_

" _The third child is here and he is currently fighting the Angel using Eva-1,"_ Lilith wasn't surprised to hear this. Gendo had told her and, of course, she had told Rei about this.

Speaking of her daughter Lilith wondered what she thought about him. Even she was curious about how the third child had ended up. Geno never really talked about on how any of the children were doing when he talked to her. With Rei, she could just ask her but that wasn't a case with either of the other two children. " _Rei have you managed to talk to the third child in any way?"_

" _I made contact with him before the Angel attacked for a split second and again when the Commander pulled me out to get him to pilot the Eva,"_ Rei remembered the look he gave her when he watched her in pain. As soon as he was off to pilot the Eva she made contact with his mind one last time. " _I do think on some level he might know what he is but he seems to be suppressing the thought of it."_

On some level that was understandable. Honestly, given both him and the second child are originally human she suspected they would suppress it if they found out about it. Rei being as she is was far closer to her and with a soul that was directly ripped from her own would have no reason to suppress the fact. " _Should I tell him the truth about everything?"_

There was something that Lilith had to think about. On one hand, telling him everything might be a bit too much. Especially his mother which given how young and how long it's been he might just have forgotten about. What's worse telling him that Yui planned to get absorbed hoping for his father to dump him would probably not be best along with the knowledge that he was a Nephilim and he had to help start at least three different plans for Third Impact. " _Just tell him about his nature as a Nephilim and about the truth of the Angels and why they are attacking us the rest we'll have to tell him later."_

Suddenly Lilith felt a surge from somewhere as the presence of Adam's child was suddenly gone. If she could she would have sighed in relief at the death of one of their many foes. She didn't know how many would come but it was a start. ' _I'll need to keep a close eye on Gendo and hopefully see if I know just what the timetable is.'_

* * *

Shinji found himself within a mist covered haze of darkness all around. For a moment he saw a flash to when he was younger. Watching as his mother was talking to his grandfather. "The development of Eva-1 would be much easier with these notes," Yui held several papers in her hands. "Thank you."

His grandfather gave her a smile. "Your welcome and tell my grandson I said hi."

"I will," She waved him off as he left the room. After almost a full minute Yui started to laugh. This wasn't a kind laugh no the way it sounded sent chills down Shinji's spine. "The fool has no idea what I am actually planning to do."

The scene disappeared before him as Shinji awoke with a gasp. He was starting up at a white ceiling wondering how he had gotten here. ' _That's right I was piloting the Eva and fought that Angel.'_ As he thought about it his mind returned to the girl that his father was going to make pilot the Eva if he didn't. The girl he had seen when he first arrived. ' _Rei was her name.'_

Just before he had gotten into the robot he had heard a voice. The same one as her own if he recalled in his head. ' _You need to know what you are.'_

He wondered just what all that was about. Did he just make it all up in his head? A logical part of him believed it to be true but something within him told him that it wasn't. Shinji was interrupted from his thoughts by the sound of Misato's voice. "You're finally up."

Shinji turned his head to her. He caught sight of her outfit that she was now wearing. He was sure that she wasn't wearing it last time he saw her. "H-how long was I out?"

"About three days." Misato response made him shot up in surprise. He had been unconscious for three days!

"Th-three d-days?!" He couldn't believe it. Shinji wondered for a few moments on what he had gotten himself into. His father just called him up and effectively got him into a war zone with dangerous beings without any prior training. ' _Why me?'_

For a brief moment, he wondered if he could get out of this. That was quickly pushed back as he realized he had no idea what he was going to do. Furthermore, it wasn't like he could even go back to his old caretaker either. Shinji whispered under his breath at this. "He effectively drafted me into a war I wanted no part of," Seeing he was stuck he might as well learn what he was going to do. Turning to Misato he asked the question on his mind. "So, I'm I just going to stay here at the base?"

Misato shook her head at this. She gave him a wink. "Nope, you'll be staying with me."

* * *

There was only one thing that Gendo disliked about his job. Meeting with the overseers of NERV. Officially the organization was under the eye of the U.N. In truth SEELE the group who had in various incarnation influenced the world to differing degrees serve as the true overseers of NERV. Gendo looked at the pillars that they each used to communicate. "The Angel has been dealt with as you know and while a few rumors have popped up on the internet no one is putting much thought into it outside the conspiracy groups on the extremes of political thought."

"Perhaps, but in this day in age, the extremes have more of a voice than ever before." SEELE members knew from experience how hard it was to maintain control that they had because of them. The Second Impact and the wars that followed radicalized many sets of the population.

In a way, this was used by SEELE to help them set up NERV and its predecessor for just this task. After all, a few anonymous funding to several of the violate groups on the fringes along with the threat of growing dictatorships set up everything for the U.N. to take a more active approach in the military. "It doesn't matter by the time they find out the truth of the threat no one would be questioning the legitimacy of NERV."

Gendo continued to stand in the middle of the floating obelisks that SEELE used to talk. He knew who each of them were so there wasn't any reason for them to do so. "If I may the one who took out the Angel was your son correct?"

There was no change in Gendo expression but he knew who was asking him that. One of the few members on the SEELE inner council he actually feared. His father-in-law and Shinji grandfather. "That is correct."

"You know I think I might pay him a visit." Gendo tensed up for a fraction of a second at this. The other members of SEELE remained silent but he knew they were likely grinning and snickering at him.

He wasn't going to give them any more satisfaction in their attempts to drive him uneasily. Though he made a mental note to keep a close tab on any documents pertaining to his son. If his father-in-law got to him there was a chance he could end up turning him against the scenario. "If you don't mind I would like to return to the subject at hand."

"Very well Gendo," They did have a lot to talk about when it came to the report they were given. The U.N forces having been proven that they can't defeat an Angel was going to be moved into a supportive role as they had envisioned. "We will have all command for the Angel War given to you if any of the local forces have a problem with it let us know so that we may correct it."

A double-edged sword if he ever knew it to be. He'll have command of the U.N. forces but he knew where their loyalties lay. A very subtle way of them reminding him that he was to serve them and not an agenda that he had. They were right not to fully trust him. "Thank you."

Unknown to either of them or even Gendo someone was watching them. No matter how secure Gendo or SEELE believed this room was it was still part of the Geofront. Lilith watched silently as they spoke to one another.

* * *

Ritsuko looked at Rei as she walked into the medical ward. Most people at NERV were fed some story about her being the niece of the Commander's friend. A tale that many accepted though a few were known to question it. She knew the truth of the matter and in many ways, she actually felt pity for her.

Yui Ikari the Commander's late wife had made a whole tank filled with clones of her. Each one a mix of her DNA, or more accurately what was once her DNA, and that of the thing in the basement. Each one of them was basically sick due to their creation and had to remain in LCL fluid to stay healthy. ' _Too late to make any adjustments to stabilize her.'_

She would never say this out loud but Ritsuko hated how obsessed Gendo was with his late wife. Just looking at Rei who was basically designed by Yui to look like her was proof enough to her that the woman was likely utterly narcissistic. Perhaps she was even a bit cruel for having a girl like Rei be forced to suffer just by walking out of the tank.

Whatever the case she had in her hand the medication that Rei was supposed to take. A means to help slow the pain and help her with the side effects until they brought her in for her LCL baths. Medicine that unaware to either her or Gendo that Rei never took. Lilith had corrected all the genetic mistakes rendering the need for it pointless. True before she had made contact with her mother and learned everything she still acted as she needed it. A leftover mark from her first life when her body was close to breaking apart.

Still, she had to play the part just to keep suspicions off of her. If Gendo ever knew the truth he would be demanding answers. Answers that could very likely break him and either cause him to be replaced or worse. He might just side with Adams Angels and doom the world in despair. "Rei I have your medicine for you."

Rei turned to her as her eyes fell on the medicine. Ritsuko placed it on the counter next to her and turned to walk away. "Doctor Akagi is the Commander's son out of the medical ward?"

Ritsuko looked back at Rei with a raised eyebrow. She didn't expect Rei to ask about the boy. Perhaps she wanted to thank him for deciding to pilot and saving her life? ' _Weird, I had always pegged Rei for a death seeker.'_ Another thing that made her hate Yui and pity Rei. The pain that she was forced to suffer and her carelessness for her own life was worrying in itself. If this boy had made her rethink it then she was silently grateful. "Yes, he is currently living with Misato."

The blue haired girl gave her a nod. Lilith had told her that out on everyone at NERV she believed that Misato was the closest she could trust. If Shinji was going to learn how to properly use his Angel powers when he awakens then Rei had to train him. It would be easier if Misato was in on it and aware of the truth. "Thank you, Doctor Akagi."

Ritsuko turned and walked away. For a moment she thought about Rei living conditions. The building that Gendo left her in was practically run down. Hearing that Misato was given custody of Shinji made her remember the first time she saw the girls living arrangements. ' _For being your all-important key to everything you are treating her like she doesn't even matter to you!'_

She could bring it up with him though something told her it wouldn't matter. Perhaps she could talk to Misato about it. "Who knows maybe Shinji would have a positive influence on Rei."

* * *

Asuka bit walked into the room for training as she overheard several of the staff of NERV's German branch talk amongst themselves. A bit curious as to what they were talking about she moved closer to hear them. "I can't believe it Tokyo-3 was attacked and their Eva pilot took out an Angel!"

"Wait I thought you said that their pilot was injured?"

"That is true but my cousin told me that it was actually a new one the son of the Commander I believe."

No way was she hearing this. Some new pilot had managed to take out an Angel without any training. Asuka was both impressed and had a bit of a hit to her pride. Yet, something within her wanted to go and meet this pilot. She couldn't answer as to why this was though. "I want to head to Tokyo-3."

The staff all turned to her a bit surprised by her sudden demand. The personnel looked at her other for a few seconds wondering if they should. After a while one of them decided to speak up at her request. "I'll see what I can do about that."

* * *

 **So, I figured I shouldn't write the first battle due to it effectively just being as I was planning a near copy of the anime. My apologies for skipping it. Though, that shouldn't be a problem as we go on. Anyway, I might hold off the next update for a while or I might not. I do have quite a few stories after all. We will just see how my inspiration goes.**

 **Cya all next time.**


	4. Chapter 3

**Surprising even me, I managed to make another chapter. I think its because of how easy it is to write when I get going. Perhaps, I am finally out of my writers light block.**

 **Thank you Scattershot98, Reishin Amara, S-01, and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix (?), Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

The call he had gotten was unexpected. Yet, He saw an opportunity and was quick to take it. After a half an hour of negotiations, it seemed he finally had the Second Child under his watchful eye. They were just going to have to make a few changes to help with accommodating her. ' _Misato has an extra room in her apartment and perhaps…'_

He was cut from his thoughts as Ritsuko walked in. The chief scientist looked at him with a bit of an enraged look on her face. "What is the meaning of this?"

Gendo knew what she was referring too. Truthfully he knew about how attached the doctor had gotten to Rei when she found out about the clones. The creations of his late wife that she made in order to contain the soul of Lilith. At first, she was rather fearful of her and she was rather justified in that thought. She was afraid of the fact they had an actual Angel on par with Adam in their mists and walking around. Although after seeing how empty and almost how broken and, in a certain way, sad she quickly became attached and worried for her well being.

As of now he could actually see her almost adopting Rei if there was an option. It was both bother a benefit and a problem. He didn't have to worry about her abusing Rei or being fearful of their relationship. The negative was that she was vocal about his treatment of her. "I did tell you to read the whole thing over when you agreed to it, Doctor Akagi."

"You know the building she is living in isn't safe so how could you leave her there?" Ritsuko wrapped back at him. Gendo had chosen it for a few reasons. Each one rather subtle though in the end, it was rather cheap and not as if anyone would question it.

A thought crossed his mind. The Second Child was rather competitive. She was coming here to likely meet with his son due to him taking out an Angel. Perhaps he could use this to further ensure things went as he hoped. "If you wish I might be able to allow something about that."

* * *

If there was one thing Shinji dreaded it was going back to public school. The last time he went there it was a slow agony. When he learned his father had arranged it Shinji just rolled his eyes at this. Of course, his dear old dad was making him do this. ' _At least things aren't as bad as they were.'_

A few of the students were actually, friendly with him. Two of them being Kensuke Aide and Toji Suzuhara who knew that he was a pilot and about the truth of what had happened when the Angel attacked. Considering the news was trying to spin it as some sort of freak monster created in the aftermath of Second Impact, and a lot of people seemed to by buying it on the internet, this was surprising. Kansuke explained that his father and grandfather both work for NERV so he was able to discover it from their reports.

By the end of the day, Shinji was actually a bit hopeful. People did comment on his dual colored hair and eyes but no one really made a fuss about it. although a few did point out that he was kind of like the other new student they had gotten a year ago. Shinji looked at the empty desk next to him. It was where Rei would sit in the class. "Shinji," Shinji looked up to his homeroom teacher as class was just about to end. "I need you to give Rei her homework for the day."

Shinji looked at the teacher who handed him Rei's homework. According to Misato, the school was informed about him being part of the same program at NERV but nothing much beyond that. It seemed the same was true for Rei. So, it would make sense for him to be chosen to give Rei her homework. ' _Wait, where exactly is it that Rei lives?'_

The sound of the bell ringing caught everyone's attention as the class soon exited the room. Shinji pulled out the phone that Misato had given him. After waiting for a few minutes Misato picked up on the other end. "Hey, Shinji what is it?"

"Do, you know were Rei happens to live?" He put his homework within his school bag as he held on to her homework. Come to think of it he was wondering a lot about the girl lately. He had seen her not long after he got to Tokyo-3. In a vision of all things before he actually met her in person. It was mysterious and just before he had got into the Eva he had thought he heard her voice again in his mind. "I have her homework and I have no idea where I'm supposed to go to give it to her."

"I don't know myself though I'll look it up for yeah," Misato answered as Shinji waited for her response. After finally getting the address he set out for the train station.

* * *

Misato wanted to make sure she was hearing this right. Ritsuko had called her to talk about the prospect of her taking in another tenant. Well, actually she wanted to see if she wanted to take in two of them. The first one was the transfer pilot from the German branch, who after a lot of pressure from Gendo after finding out they wanted to come to Tokyo-3, was going to be staying here. The second one was the more surprising of the two. "You want Rei to move in with me and Shinji why?"

Ritsuko pulled out a picture of a run down and half collapsed building before her. "Because this is the state she lives in and I can't let her stay in such horrible conditions," Ritsuko would have brought her two her place if she could. The problem was as she found out that she couldn't when Gendo made her sign on as Rei watcher and caretaker while at NERV. Something told her he actually expected this. "I can't due to my contract and no one else wants to due to having to have Section 2 agents posted with them."

"And wouldn't that include me?" Misato would rather not have those men watching her. A few of them creeped her out.

Ritsuko shook her head at this. She had asked the commander about that tidbit after noticing their unsettling gazes to her. It was the only way he would sign off on her transfer. "As a trained member of the army, there wouldn't have any need to do so."

Well, that was one good point. Though Misato did question letting a young boy and a girl who were teenagers stay in the same building together. Especially given how off and emotionally broken Rei seemed to be. "What about the other pilot who are they?"

Ritsuko gave her the file. Opening it Misato was greeted with a picture of Asuka and made note that her eyes seemed to have misshapen pupils. The first thought that crossed her mind was having to house another girl. The second was the strangeness of the three pilots. She blinked at her deity report. "Wait, she's only been eating raw meat for years isn't that unhealthy?"

Ritsuko shrugged her shoulders at this. She tried to get an explanation on this but they didn't have much of an idea as to why. They suspected side effects of Eva piloting but exactly how was never looked into. "Apparently she has a trouble eating cooked meat and for some strange reason doesn't get sick when eating meat raw," Misato continued reading as the only other thing they commented on in her report caught her attention. "Along with a few other mutations."

"She has sharpened teeth?" Misato looked at Ritsuko to make sure that this wasn't a prank. Ritsuko just gave her a serious look. "You're serious."

"I had a similar reaction when I found out." Ritsuko was certain something was off to cause this sort of change. The moment she could she was going to look into getting a blood sample to test it and perhaps even one of Shinji's to compare it too. There was just something off.

Mistake closed the file as she thought this over. She had an extra room that she mostly just stuffed with some junk but could be fixed up. Still, sticking two girls to share it could be a hassle. ' _Or maybe not given how passive Rei is.'_ A sigh escaped Misato's lips. "I guess I'm going to have to clean up that extra room for the both of them."

Ritsuko had a smile at this. She knew she could trust Misato to help her. "Thank you."

* * *

The part of the city that Shinji was walking through was mostly torn down. Demolitions equipment lined the area along with the rumble from several of the buildings that had partly collapsed. ' _Does Rei's family live here?'_

He pulled up the paper with the address given to him just to make sure he was correct. The building where Rei lived was half fallen in. This was supposed to be owned by NERV and yet it looked like it was barely livable. Shinji took note of the Section 2 agents standing watch outside the building. They were practically the only people here. They seemed to just barely acknowledge him as he walked into the building.

Silence was all he could hear. There was no sounds or signs that anyone had lived here. It was like a ghost town. "Second-floor room five."

That was the apartment that Rei had. He was actually feeling very bad for her. Having to live here wondering if she even had things like running water. Pushing away his concerns he stood in front of the door to her apartment. Not a sound could be heard. "Rei are you there?"

He knocked a bit before noticing that the door was open slightly. He pulled the door open noticing that the lock was broken. Who lived like this in such a place? "I have your homework from school…" His eyes went wide as he watched Rei walk out of the bathroom without anything on and only handing the towel in her arms. It took him half a moment to realize that he was staring at her. "I-I-I s-sorry I-I should have w-waited."

Rei looked at him with confusion. She didn't know why he was acting like this. Rei having to undress for each of her LCL sessions hadn't quite grasped the concept of modesty. As far as she knew there was nothing wrong. "Why are you sorry?"

Shinji wondered if she was joking. After a few moments, it turned out that she wasn't. "I-I walked in on you while you were naked."

"Is that a problem?" Hearing this caused him to go wide-eyed in surprise. She really didn't have any clue about what he had just done. "Should I get dressed?"

' _How is that even a question?'_ The question on how Rei had such a disregard for modesty aside he would rather not listen to the small voice in his head telling him to take a look.

Shinji looked at the rundown apartment wondering why Rei was forced to live here. The buildings around it were all torn down. This one looked like it was half fallen apart as is. "I'm clothed now," Shinji turned back to see Rei in a simple pale blue dress. "I see you were chosen to bring my homework to me?"

He gave her a nod as he tried to fight back the image of Rei's naked form out of his head. A task that he was failing at completely. Embarrassed he tried to look away as he handed them to her. "Y-y-yeah, h-here."

Rei took the papers in her hand as she looked at them. Curious as to his behavior she reached out with her A.T. field to figure out what was wrong. ' _He thinks I'm pretty?'_ She felt her heartbeat race for just a moment at this. It confused her though she won't mind if she heard it again. "Thank you."

Shinji decided to left the apartment now that his mission was done. At least until Rei grabbed his arm and with surprising strength pulled him to her. "W-what?" He was suddenly facing her with his dual colored eyes looking straight into her red ones. ' _They are like rubies.'_

"Shinji what do you know about why we are fighting the Angels?" Rei's voice pulled him out of the minor trance that he was in.

Taking a moment he realized what she had asked him. He knew as much as the document that Misato gave him. "T-they caused Second Impact and if we don't stop them Then they'll kill everyone else."

Rei shook her head at this. Then again Gendo was likely to not tell anyone about everything he knew. Nor did he knew all it himself. "That's only partly true, Second Impact was caused by the Angel Adam but the war isn't as you are told."

Inwardly Shinji wanted to laugh at this. Of course, his father wasn't telling him everything. At this point, he wouldn't be surprised if he had remarried. "What is the truth then."

Rei sat on her bed and motioned for Shinji to join her. He hesitated for a moment before sitting on the rather plain and somewhat broken mattress. "There are actually two lines of Angels the one that we are fighting is the spawn of Adam, who are seeking their progenitor in order to preterm there own Third Impact as a means to terraform the planet for themselves."

That sort of cleared some things up. All the document said that the Angels were planning to wipe out humanity to conquer the world. Finding out that their goal was to locate their creator and terraform the world explained their motive. "Wait, you said there are two lines of Angels what is the other one?"

"Ours," Rei simply stated drawing confusion to Shinji. The blue haired girl continued on while his mind was racing, "Lilith is Adam's counterpart and she's been here just as long as he had it was her blood that mixed with the primordial oceans and created all life on the earth," She closed her eyes as she knew that the next part was going to be a lot to take in for him. "When she awoke Second Impact had already passed and in hopes of preventing Third Impact she created her own Angels though a fusion of both Angelic and Human in both body and soul," She turned to him looking him right into his eyes. "We are the Nephilim of Lilith."

Shinji looked at her not knowing what to say. It sounded outlandish. He wasn't some kind of half Angel monster! ' _Why do I sound so unsure though?'_ The image of the thing from his dreams returned again as he tried to push it away at this. "Y-y-you're joking right?"

Rei looked at him before deciding that it was best to show him. To Shinji's shock two white wings shootout. They were long and gave off the appearance of being connected to her body like they were apart of her skin and back yet they were still just wings of light. A trait all angels had regardless of their lines. Shinji looked at her before the image of the thing from his dreams filled his vision before he fainted.

Shinji awoke as his eyes blurred in a haze. When his sight finally clear he was meet with Rei looking over him while he was in her bed. At first, he felt himself panic wondering what had happened before the memories hit him of what happened. Rei had told him everything and now he couldn't deny it. That thing he saw in his dreams was him. "H-how long was I out?"

"Only a few minutes," Rei could sense that he was starting to accept the truth. The hold on he had placed A.T. field was starting to weaken. Though it was still dormant at least it wouldn't be suppressed by him when he awoke his angelic nature.

So many questions ran through Shinji's mind. Why was he chosen to be one of these Nephilim? Furthermore wasn't he born human? "H-how did we end up like this?"

Rei looked on at him as Shinji started to realize the position they were in. A slight blush formed on his face at this. "I only know that both you and the Second Child were given it while you were still young allowing you both to develop into it as you age," That might explain why he couldn't remember it given how much of it he had forgotten. "I on the other have was made the way I was made from Lilith's own flesh and my soul birth from her own."

He didn't know much about Angels beyond what he had been told so far by both Misato's report and Rei. Even so, the way she was talking about Lilith made it sound like she was her mother. Still, She was awfully close to him and try as he might he couldn't push out his thoughts. "So, are you like her daughter?"

"She calls me as such and has been the only parent I have ever known," Talking about parents she knew she should tell him about his. Especially just how cruel his mother really was.

A terrifying thought crossed his mind though. Did his father know that he was Nephilim? Rei looking at his expression noticed the panic and the slight increase in his breath as the horror of this crossed his mind. She made contact with her A.T. field to know what was on his mind. "Your father has no idea what either of us are as far as he knows you are still human."

Shinji's eyes widened at this. He was relieved to know that his dad wasn't using him for some kind of science experiment or a weapon. He literally wouldn't put it passed him. "Wait, how did you know what I was thinking?" He paused before realizing it had to be something that she could do thanks to her Angel powers. "You can read my mind?"

"In a since, I learned how to pick it up by reading your A.T. field it's something mother first taught me," Rei explained as she pulled back her field from him. "Like each Angel, our A.T. field has different properties and each of us have different abilities though like my mother I share the ability to read people via their A.T. field and contact them."

Suddenly he was starting to remember the position they were in. The talk about being able to read him made him go bright red. ' _Why do I smell blueberries?'_ His eyes widened as he realized he was smelling Rei's scent. To his surprise, Rei moved ever so closer to his face. ' _It can't be…'_

His mind went blank as Rei kissed him. The beating of his heart started to increase while unknown to him Rei felt her own heart increasing as well. She had no idea what came over her but a small pull told her to kiss him. For a second nothing happened before he kissed her back and for a brief second the two of them were actually kissing the other. When Rei pulled back the two looked at one another's eyes without saying a word.

Silence gripped the two of them as they simply looked unsure of what to say or even do. Finally, after seemingly a full minute Shinji finally spoke up. "I-I-I got to get b-back b-before Misato c-comes looking for me."

Rei gave him a nod as she moved off the bed and watched him leave. For a few moments, Rei continued to look on before putting her hands on her heart. ' _What is this feeling?'_ She closed her eyes as she recalled the feeling of the kiss. Her wings reappeared as her A.T. field fear out for a brief moment. As soon as it came it was gone. ' _Maybe I should ask my mother?'_

* * *

The Evangelion Unit-1 looked too anyone like it was just a big machine. The few that knew the truth about what they were made with an organic base would still have to agree that in function they fit the part. However, the darkest and most well-kept secret was that each Eva Unit held a soul of someone. This was why so few of them even existed. Each one of them was a prison. All except for Eva-1.

A lot more love and care went into its creation. For while the others were just made with a war in mind against the Angels this one serves another purpose in mind. Strictly speaking, it was far more developed and complex organically almost being a full grew angel outside of a few missing parts. After all, its soul didn't want to be trapped within a walking prison.

' _Something is wrong,'_ Yui awoke from her sleep having dreamed silently within her new body. The actions of using the Eva unit had slowly awoken her from this sleep. Everything was going as she had hoped. That is until she finally realized one thing was wrong. ' _My son isn't as I need him to be.'_

Yui felt something off with him. She didn't like unknown variables and she had planned for a host of them. If anyone was looking they would have noticed Eva-1's fingers twitch in annoyance. An action that Yui took note of. ' _What in the world.'_ It took her a few moments to locate why this was. If she could Yui would grin in joy at the surprising development. ' _An S2 organ!'_

There was one thing Yui couldn't seem to replicate when they were making the Eva's from the genetic remains of Adam or Lilith. The S2 organ was both biological and at the same time seemed almost magical in its nature. In theory, each of the Eva's could develop one. Though due to designs only Eva-1 was able to make any use of it as Yui was able to supervise it's making herself. ' _It's still developing but it would soon be functional and with it the first step of my plan.'_

How this came to be Yui didn't know but she wasn't going to deny such a gift. With the way things will go she suspected that she would soon have the others find her the remaining two keys for her plans and with them she could finally complete her vision.

* * *

Shinji walked into the apartment. His mind was still consumed on the realization that Rei had given him. He wasn't human like he had thought he was. It explained a lot about how he was. Why he had randomly developed his weird physical traits and his strength. Shinji looked at himself as he flexed his hand. ' _What does this even make me am I still who I am?'_

It seemed like an easy answer. However, the problem set in when he remembered that he had no idea what he was his whole life. He lived it thinking he was human when he actually wasn't. In a way, it seemed he was almost living a lie. "Oh, Shinji your back I had almost thought that you had gotten lost," His caretaker voice pulled him out of his thoughts as he watched her moving out some boxes from her extra room. "Now, I need your help getting the net room set up as a bedroom."

"Someone is moving in with us?" This was a surprise. Barely a week in Tokyo-3 and already things were changing around rather quickly. "Who is it?"

"Oh, Rei and the pilot transfer from Germany." Misato response caused Shinji to blink in surprise. He had just finished talking to Rei not too long ago and already they were going to be living together.

He was happy that she was moving out of that terrible building and he could get some answers on the whole Nephilim business. His mind, however, couldn't help but picture the kiss they had shared. The feeling on her lips on his and her scent on his nose still lingered. The thought of her living with them made him feel happy. "Wait, a pilot transfer from Germany?"

Misato gave him a nod before pulling out the picture she was given. "Her name is Asuka Langley Soryu, she's the second child and pilot of Eva-2." The thing that caught his attention was the oval-shaped pupils. He remembered Rei talking about how the Second Child was like the both of them. "Oh, and the raw meat with a yellow marker steak on it shouldn't be cook she can't actually eat cooked meat."

Eating uncooked meat sound rather unhealthy. Then again if she was a Nephilim then perhaps that wasn't a problem. "So, when will she get here?"

"I think we'll be meeting her tomorrow," Misato then remembered something. "Oh, right Ritsuko wanted you to prefer a harmonic test tomorrow as well with Rei and Asuka."

* * *

Asuka looked out the night sky as she stretched herself. Sitting for nearly two hours as the plane flew from Berlin to Tokyo-2. Eva-2 was being shipped out with the U.N. Aircraft carrier Over-The-Rainbow. Apparently, she was going to be transferred over to the main branch of NERV in Japan. ' _At least I am going to see some action hopefully.'_

She couldn't wait to see the two pilots that they had. Who knows maybe she'll see if the newbie actually had some skill outside of beginners luck.

* * *

 **Asuka has finally made it. The Nephilim of Lilith are nearly together. I can't wait to begin to write the interactions between the three of them. Now I think I have to explain something to S-01. Genetically speaking, Shinji and Rei genetic structures are altered by the angelic DNA. To some up they are not related to each other, in fact genetically speaking Shinji isn't Gendo and Yui child anymore.** **Explanations aside if you have a suggestion I won't mind looking into it and taking it into consideration.**

 **Cya all next chapter.**


	5. Chapter 4

**Hey, everyone, I'm back with another chapter! It's a little sort compared to the other two but I couldn't find anything else with it. So, apologies everyone.**

 **Thank you Scattershot98, Reishin Amara, and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Asuka looked out at Tokyo-3 as she got off the train. The fortress city that housed the headquarters of NERV. As she walked out through the crowd with her luggage she heard someone's voice in her ears. "We're all here."

Asuka blinked as she saw two figures suddenly appearing before her. The first being a blue-haired red-eyed girl with pale skin and the other a two colored eye body with grey highlights in his hair. As soon as she blinked they were gone. Asuka rubbed her eyes before shaking her head. "It's nothing just my mind playing tricks on me."

* * *

NERV headquarters was abuzz as they had to get everything ready for Eva-2 and it's pilot. The Evangelion Unit was scheduled to arrive within a week time along with its equipment. Shinji followed Misato as Rei followed along. They were pulled out of school for the harmonic training. ' _The new pilot should already be here,'_ The last of the Nephilim of Lilith. Shinji didn't get much from Misato but what he did learn was that she had been piloting the longest out of all three of them. ' _She's probably better skilled then both me and Rei that's for sure.'_

As they continued to the hangar bays for the Eva's Shinji felt that strange presence again like it was watching him. He looked back wondering if it was Rei but she seemed focused on what they were going to do. His mind remembered the kiss from yesterday still fresh in his mind. Pushing it away he continued to look forward.

Standing out looking over both Eva-1 and Eva-0 was Ritsuko as she went over the few of the papers she was given on Eva-2. Seeing how she would be reviving the Evangelion within a weeks time she had best get familiar with it. Catching the sight of Misato, Rei, and Shinji out the corner of her eyes she closed the files and turned to them. "You're both a little early for the harmonics test."

Misato shrugged her shoulders at this. "I figured both Shinji and Rei could meet the new pilot they would be working with," Come to think of it she wondered where she was. "Hey, Ritz do you know where we could find her?"

"Why you don't have to look no further!" At that, the group turned as Asuka came walking out with a yellow sundress on. The German pilot paused as her eyes fell on both Rei and Shinji. ' _Was zur Hölle!_ '

She had thought that they were nothing but a random mirage. Instead, she was staring at both figures from her little vision. "Shinji, Rei this is Asuka Langley Soryu the Second Child," Ritsuko introduced as Asuka continued to look at them making sure she was seeing this correctly. "Asuka these are our pilots Rei Ayanami the first child and Shinji Ikari the third child."

Misato looked at the three pilots. The first three children who were stated to save humanity. Each one of them just looked different from what you expect. Rei ice-blue hair, albino-like skin, and red eyes. Shinji's heterochromia eyes each of an unnatural color and the grey highlights which were naturally as he informed her. Finally, there was Asuka who could almost pass for normal unless you got in close to see the shape of her pupils and when she opened her mouth and you could see the teeth of a predator. ' _You know if I didn't know any better I would question if they were even human.'_

Asuka wanted to know what was going on. She wanted answers on why the two of them were here when she heard a voice in her mind. " _I will explain everything just don't bring it up."_ Asuka turned to Rei as she felt like it was her doing.

It seemed dumb to ask. As there was no way that this was happening but Asuka did it anyway. ' _Are you reading my thoughts?'_

" _In a sense."_ Asuka had a lot of questions. She was going to get answers and she wanted them now. Rei sensing this turned to Misato. "Captain Katsuragi would it be alright if me and Shinji talk to Asuka in somewhere private?"

Rei knew of a few places in NERV were Lilith had confirmed that wasn't bugged or under watch. The medical ward being the largest and generally the most devoid of human life at any one time. NERV has surprising good safest precautions for everyone with the exception of the pilots. "Sure just don't wander out of NERV alright."

* * *

Shinji looked between the two girls wondering what was going to be Asuka response to what she had heard. The first thing Rei explained that she had contacted Asuka via her A.T. field when she felt her enter the city. After that, she then told Asuka about her nature as a Nephilim along with what that was. "So are you telling me that my teeth, my eyes, and my eating habits are all due to me being a Nephilim?"

Rei gave her a nod on confirmation. "That is correct."

A few moments passed before Asuka shrugged. Unlike Shinji, she had known something was different about her and didn't try to subconsciously repress it. "Well, I guess this really does make me special." She paused before looking at Rei with a questioning look. "Wait, why is it I can't do anything like you seem to be able to?"

"Both of you haven't awakened while I have," Rei explained as she looked at her two fellow Nephilim. "And furthermore not all powers are the same for each Angel as you both would likely develop different abilities compared to me."

While she was a bit annoyed that she was being told that she couldn't use her cool Angel abilities she at least had something to look forward too. Now the only question she had was how to unlock them. "Alright, and why all the secrecy?"

Shinji was actually in agreement with that. While he never wanted to tell his dad about it he did want to know why Rei was awfully quiet about it. Rei thought it over before she spoke. "If it got out about what we are then both the Commander and the committee who oversees him would dispose of us for being what we are."

The both of them froze up at this. Shinji for his part was actually surprised to learn this. Sure he fingered his father was pretty heartless but the idea that he would kill him for something like this seemed a bit much. ' _Who am I kidding,'_ The depressing truth was that his father likely didn't give a damn about him at all and don't care if he killed him. ' _Of course, he would!'_

"Mein gott," Asuka couldn't believe it herself. Though if she thought about it the whole point of NERV was to fight the Angels. Having their pilots be Angels themselves kind of defeated the whole purpose. "What's keeping us from being targeted when we awaken then?"

There wasn't an answer for a few moments from Rei. She felt a gentle nudge on her A.T. field and knew it was her mother. Now, was the time to tell them about the biggest secret in NERV. "My mother Lilith is trapped within the basement of NERV when the Magi system picks us up she will use her remaining strength to trick the system into thinking it's glitched."

The fact, that NERV held an Angel, the Angel that turned them both into a Nephilim was surprising. There was only question that Shinji could ask after hearing this. "How long as Lilith been here?"

"Ever since her seed-ship crashed into the planet four billion years ago," Officially nearly everyone at NERV believed that the Geofront was, as it was stated to the public, an elaborate underground cave system. The truth was that it was the work of alien engineering from the First Ancestral Race. "The headquarters is built within part of the ships remains and that's how they found Lilith still in a coma from the trauma of the impact that started all life on the planet."

If Gendo or SEELE knew that one of their biggest secrets had just been told they won't hesitate to end the lives of both whoever spilled it and anyone who heard it. The knowledge of Lilith was paramount to their plans and the fewer people that knew about it the better. Even Rei wasn't supposed to know everything about it even in the original plan. One of the benefits of having Lilith herself working against them it seemed. "Is that why I have this weird feeling that someone is always there?"

Shinji turned to Asuka for a second. He had thought he was the only one that had that strange feeling. With the knowledge that Lilith was kept within this place, that was actually her spaceship, it explained it to him. "Yes, She reaches out with her A.T. field to keep tabs on what happens when we are here to make certain that nothing bad happens," Rei paused for a moment as a thought crossed her mind. "If you like I could see about letting you both talk to her right now."

"How are you going to do that?" Shinji then realized it was a pretty dumb question.

Rei reached out to the both of them with her A.T. field. Echoing in both on their minds was Rei's voice. " _I figured I would do this."_

Before the two of them could comment on this for a brief moment they saw what looked like an adult Rei with a plain white dress, her hair was almost to her ankles at how long it was, he had the same red eyes with black sclera and from her back was several wings each one shaped like those that Rei had shown Shinji. " _It's nice to finally meet the two of you."_

As soon as they blinked the image was gone but they couldn't help but remember what she looked like. Shinji was stunned as he wasn't expecting that. ' _That was Lilith?'_

Rei gave him a nod. She had seen the image that Lilith imprinted in their minds. " _In a sense that is what she would look like if she had a form like us."_

' _Well, I guess that must make you a Mini-Lilith then?'_ Asuka had a bit a smirk at this.

A lighthearted laugh was heard echoing in their minds. After it ended Lilith's voice spoke with them feeling a pull all around them. " _Given that she was directly made from my flesh and my soul I think you can see it that way,"_ Even though it was indirectly Lilith could still feel their questions and could see the effects their lives had had. Asuka was accepting what she was rather easily when compared to Shinji. On a subconscious level, she had always known she was different. Shinji was still in a very turbulent state and was trying to figure out his identity within all of this. " _I am certain you have a lot of questions."_

Shinji's mind was filled with them. The one that was first on his mind was simply why him and Asuka? Why was it that they were chosen and what would they do when the war was over? Before he could ask his question the three of them were cut off by the sound of Shinji's phone ringing. Pulling it out he saw that it was Misato. "Shinji where are you Ritz got Eva-1 and Eva-0 ready for your's and Rei's sync test."

Just when he wanted to get some answers too. He let out a mental sigh before answering back. "I'm coming."

Lilith knew he was disappointed. She could tell what he was hoping to ask her. The truth was she wasn't sure about telling him about. Especially given she'll have to tell him about SEELE and their plans. Of course, that would quickly open up a whole rabbit hole about the Evangelions and finally come to his mother. With how fragile his psyche and sense of himself was this would break him. " _I'm sorry we can still talk later."_ With that Rei pulled off her A.T. field from the both of them. " _Rei, you and me need to have a talk after your test about that thing from yesterday."_

* * *

A deep breath escaped his mouth as Shinji readied himself as the test began. The LCL fluid flooded in with the metallic smell of it hitting his nose. "Alright, Shinji let's begin synchronization in three, two, one."

As the test started the soul within the Eva took this time to look at her son. Yui noticed that something was off and as the synchronization rate increased she was able to take a look at him. ' _Outwardly his eyes and hair has changed and inwardly…'_ If she still had her eyes they would be widened as she saw an extra organ. One which only Angels had. ' _An S2 organ?!'_

It was located in his chest but it was there. A fully developed S2 organ just like an Angel. It was mostly dormant only working on a low amount but still the way it was attached meant that it wasn't transplanted into him. Shinji had grown the organ in his life. As the ratio reached just shy of forty Yui finally could take a glance at her son's genetic structure.

For a moment nothing happened as she looked at it. She checked it three times to just make sure it was real. ' _This can not be!'_

The synchronization ratio started to fluctuate as Yui was mad. This was something she did not suspect and she was sure that something had a hand in it. Before she tried to suppress the connection completely she stopped as she noticed something. The S2 organ, Eva-1's S2 organ, was reacting to Shinji's presence. ' _Could it be..'_ She instead let up and allowed the rate to return to its previous level. ' _It is it's glowing ever slowly due to him.'_

That explained how the Evangelion had developed the organ. It was reacting to her son's new physiology when the synchronization was at a high enough level. This wasn't what she expected and yet Yui could work with this. ' _Still, how exactly did my son end up like this?'_

The test came to an end as Yui retreated within the Eva. Her mind ran through several scenarios and possible causing until she finally came to one that seemed rather likely. This worried her greatly if it was by some possibility the reason for all of this. ' _I must be careful.'_

Regardless she was going to have to play a part. Perhaps she could use her son's new nature to her advantage. Dark thoughts formed in her mind as new plans formed.

* * *

The shower water fell over Rei as the LCL was washed away from her body. She closed her eyes as she felt her mother touch her A.T. field. The ancient Angel knew that she had wanted to talk about what had happened yesterday. " _You kissed Shinji."_

The memory of the event flashed in Rei's mind. She didn't know why she did it but she liked the kiss. At that moment she moved her hand to her lips. ' _I did and I felt this strange feeling afterwards.'_

Lilith knew that there would be a natural pull between the Nephilim. A way to get them together and to work together. She didn't quite think that it could have a hand in getting them together. Not that Lilith was complaining as she was actually what one might call a shipper. " _I think my little girl has found herself a mate!"_

Rei was confused by her choice of words. She immediately went with the few documentaries that she was able to watch thanks to Ritsuko. ' _You mean I want to mate with Shinji?'_

At that Lilith immediately realized that Rei thought she was using human terminology. Lilith was suddenly embarrassed at this for forgetting this fact. " _No, that's not what I meant I think the humans call it wanting to be his wife or something,"_ Though knowing that Shinji was a teenager and her daughter rather weak understanding of proper human interactions that might happen. " _Also, if you do that please at least wait until you are a little older I don't think I'm ready to be a grandmother just yet."_

' _I can't have children though,'_ Rei understood the first part somewhat. Though the second part just seemed so strange. She had asked Ritsuko about it once and she had stated that she didn't have the organs needed for such a thing.

Silence came over from Lilith's side for a few moments. " _You do know that your body does have the organs for that right?"_ Sure the other clones were so bad that they actually developed a vestigial S2 organ in its place. " _Your body is genetically corrected meaning it's developed all the proper organs in the right places plus a working S2 organ."_

Rei was actually surprised to hear this. A thought came over her as the possibility of her being a mother crossed her mind. The image if her having a child was strangely appealing to her. Perhaps it was because she thought she couldn't become a mother and was now told it was possible. ' _But why don't I bleed down there?'_

Lilith was actually confused by what she meant. Looking around with her A.T. field she touched Ritsuko's assistant Maya to see what she knew as she was the closest female to her daughter's location. If she could she would wince in pain for the females of the species. " _Yeah, I think you don't do so because of your Nephilim physiology,"_ Lilith then thought about the other female Nephilim. " _Also, you might want to tell Asuka about that as well."_

A nod came from Rei as she turned off the water. Her questions about the feeling had been answered though how she was supposed to do know was a question in of itself. Thinking about it perhaps she could asked Misato. ' _Before I forget Doctor Akagi has gotten Misato to become my caretaker and I'll be moving in with her, Shinji, and Asuka,'_ The good thing about this was that she wasn't going to have Section 2 guards on the lookout for her. While she was safe to use her powers within her apartment Rei always knew that one slip up and they could discover her secret. ' _Do you think I should let Misato in on the secret when I move in?'_

" _Not immediately though you should start telling her about it when either Asuka or Shinji awaken,"_ A nod of understanding came from Rei as she tried off and put back on her simple outfit.

* * *

The trip to Rei apartment was rather short. Much like Shinji remembered and like Ritsuko had told Misato the place was falling apart. Rei only needed to fill a duffle bag as she barely had much in the way of possessions. When they got to Misato apartment she led them to the spare room. "Sorry about it being a mess I had to improvise."

There were one futon and one mattress that was on what looked like something of a few boxes and a small drawer. Rei placed her duffle bag in the mattress. Seeing as she used to live in worse conditions this was a step up. "It is fine thank you Captain Katsuragi."

"You can just call me Misato," Misato turned to Asuka who have her luggage placed off to the side of her the bed. "Oh and Asuka the meat packages with a yellow mark are for you in case your hungry."

Asuka gave her a nod before Misato closed the door. A few moments later both her and Rei started to unpack. "Looks like you and I are roommates Mini-Lilith," Asuka crossed her arms for a moment as she looked at the small amount of stuff that Rei owned. The girl sort of creeped her out by how emotionless she seemed to be. ' _It's almost like a living doll in a way.'_ The door opened up as Shinji walked on in. Almost as soon as he did Asuka shot him a glare. "You know how to knock!?"

Shinji glitched as she screamed at him. Her teeth gave her a rather intimidating look when she was mad. "S-s-sorry I was j-just coming to ask what you both want for dinner."

In hindsight, he probably should have knocked first. He was living with three members of the opposite sex. Two of them happen to be Nephilim and if he suspected very likely had enhanced strength just as he did. "I'm ok with anything as long as there is no meat," Both Asuka and Shinji turned their attention to Rei. "I'm a vegetarian."

Asuka turned back to Shinji with Rei having unknowingly diffused the rising tension. "I can eat anything that is not made with cooked meat," The foreign pilot raised an eyebrow at him. "Is there any reason why you are asking us about what we like to eat?"

"I kind of have taken over cooking duties." Misato wasn't a good cook by any stretch of the imagination. It took him only a day to figure that out and now he was practically the one doing all of the cooking. ' _I guess actually taking the home economics course was a good idea in hindsight.'_

* * *

Gendo stood before SEELE as he knew why he was being called in. The Second Child had ended up coming to Tokyo-3 ahead of their schedule. On the inside, he was feeling a degree of satisfaction at this. "Why is it that the Second Child is currently stationed at your headquarters?"

The NERV commander adjusted his glasses as he looked at the obelisks in front of him. He was in a very dangerous position and he had to choose his words carefully. "She wished to come to Tokyo-3 on her own in order to see our pilots and seeing how she is likely carving something then just simulations and localized tests with her Eva I figured it would be best to transfer her." He paused allowing it to set in. "In my defense, you didn't say that it was absolutely necessary that she shouldn't come to Tokyo-3 now."

"He is right," Much to Gendo surprise one of the SEELE members was actually defending him on this. "You did say that the part about the second pilot was a bit worn and fragmentary perhaps because of that we misinterpreted what it actually said."

Gendo stood as he watched each of the members put in there own thoughts. He stood there barely paying attention as he judged their responses to each other. After a few minutes of back and further, they seemed to finally reach a consensus. "Very well then as long as things do not deviate too far from what we want we see nothing wrong with this."

A small victory but one that he took great pride in. With any luck, he could use this to his advantage and pull things in his direction. Unknown to him Lilith was also taking notice of this. While Gendo saw this as a small victory Lilith saw it as a critical one. ' _The three children are together and with it, the chances of the stupid project decreases with each day.'_

"It I may seeing how Eva-4 is almost complete should we think about sending the Fourth Child over?" There was a pause as both Gendo _and_ Lilith were surprised to hear this. Gendo was not informed of this and Lilith knew from SEELE that they had only expected there to be three pilots.

After a few moments, Gendo was saying what both him and Lilith was thinking at that very moment. "There is a Fourth Child?!" He held back his emotions but on the inside, he was already weighing his options for his scenario. "Who are they?"

There were a few seconds before one of the SEELE obelisks answered. "I am surprised that they didn't inform you then again the American branch barely even reported to us what they were doing," There was a hint of anger in this members voice. "Originally we were hoping that they would make an Eva for testing new designs and alterations but after a bit of shuffling of staff they ended up finding a pilot for the Eva when they shouldn't have."

By the time SEELE found out about this the new pilot had already started training. While this did create a bit of a wild card it wasn't all that bad actually. They could just resign them to stay in America and nothing would happen. Even still, as long as everything happens as it generally should then there was really no harm. "I believe her name was Mari Makinami Illustrious."

* * *

 **Asuka has finally joined up and all the Nephilim is assembled! Oh, and yeah Mari now also a thing. I just had tto throw an unknown variable into the mix for Lilith. As long as the bulk of SEEELE's plan goes off such minor details are excusable. Fun fact, when I was writing this I was tempted to use Asuka's rebuild name over the one I ended up using due to wanting to use some of Rebuild. In the end, as I planned it out I decided to use Mari instead. Expect her further down the line to show up.**

 **Cya all next time.**


	6. Chapter 5

**I'm back once again with another chapter! Oh, and yeah I heard of Netflix getting to show the anime. Now, all we need is to wait for Rebuild 3.0+1.0. 2020 people here we come.**

 **Thank you** **Reishin Amara, Hellsink Bathhall, Scattershot98, and PrometheusDark** **for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Watching Asuka eat almost made Shinji swear off eating meat. His follow Nephilim seemed to not really have any real table manners. Having teeth that could cut through bone and metal had long caused her to forsake using any utensils. Though despite how messy she made it look Shinji just couldn't look away.

Asuka swallowed as blood dripped from her lips which she licked up. Misato looked at Asuka as she stared and put her utensil down. "I think I'm not all that hungry anymore."

Of to the side, she noticed her penguin Pen-Pen looking at Asuka with something of fear. She didn't fault him for it. The girl in question rolled her eyes in annoyance at this. "I can't help it that I eat like this you know," She took a sip of her water and caught sight of Shinji staring at her. "Why are you looking at me like that?!"

Shinji blushed for a moment in embarrassment. Sure watching her eat was both disturbing and yet also rather mesmerizing. It was in a messed up way attractive. ' _W-why am I thinking that?!'_ Asuka continued to glare at him caused him to realize that he hadn't answered her yet. "It' n-n-nothing!"

He went back to his meal as he couldn't believe his thoughts right now. Rei looking at him reaching out with her A.T. for a moment wondering what on his mind. ' _He founds Asuka attractive?'_ If possible Rei for the first time in her life felt jealousy. ' _What should I do?'_

A few minutes later after dinner, Rei was in her and Asuka room. She was lost in thought on what she could do as she weighed her options. "Hello, earth to Wondergirl." She turned her head over to Asuka who was standing over her. "You know I hate to ask but is this what you usually did while you were living in your apartment?"

Rei stood up on her mattress as she answered. "There isn't anything for me to do besides sit around in my thoughts and practice my powers," The ice blue-haired girl paused for a moment before she decided to ask something that was on her mind for a while now. "What do you think about Shinji?"

The redhead shrugged her shoulders at this. Truth be told she had only known him for a day. In that day she had seen him look so meek and introverted. He had a surprisingly good sync rate for just drafted into an Evangelion. Compared to her and Rei who been doing it for years that said something. Though the way he was looking at her while she was eating was partly disturbing to her. ' _What was he attracted to it?'_ Pushing away those thoughts Asuka crossed her arms as she now had a questioning look on her face. "Why are you asking me that?"

There wasn't a response for a few seconds as Rei looked away. Asuka got the hint as she held back laughter. "You like Boy Wonder don't yeah?"

"Boy Wonder?" It took her a moment to figure out that she meant Shinji. Come to think of it she did hear Asuka call her Wondergirl. "What happened to calling me Mini-Lilith?

Asuka took a seat on her bed as she shrugged her shoulders. "I figured I can't do that whenever without letting NERV know and plus Wondergirl rolls off the tongue you know," With that out of the way she crossed her arms and looked at Rei. "So, do you like Shinji?"

Rei didn't look at her before answering softly. "Yes, I do."

"Well, why don't you tell him how you feel?" It seemed simple enough to Asuka. Though given how stoic Rei was that might not be the case. "I mean how long have you both known each other?"

Given that Shinji was the Commander's son she suspected that they had at least three years to know each other. If she recalled she overheard the staff in NERV's German branch talking about her three years ago. "About two weeks though seeing how I was in a hospital bed for much of it at best three days."

That caught Asuka attention almost immediately. She had only known him for a few days and was already fallen in love with him. While the rational part of her mind wanted to say that it was possible another part of her was reminded that technically they were not human. "Are you serious?" For All Rei knew it could just be a crush nothing more. "Are you sure this is a bit too fast?"

Rei thought about it. True human courtship took a while but they were not human. "We each have a natural pull to each other It's so that we can come and work together," She paused as Asuka realized why it was that compiled her to come to Tokyo-3. "If experience is an issue I can have both of us know each other's lives."

"You can do that?" Rei answered with a nod. "Reading our minds, our memories, and what else can control minds?"

Rei unaware that it was a joke thought about this. Her mother was able to effectively possess someone. If her abilities were like her own the there was a possibility. "I had never tried it but I do not think it would work on us or Adam's spawn."

Asuka looked at her without a single word. She was joking about that. ' _Great, and if she wasn't creepy enough as is.'_ Deciding to get back on hand Asuka sat on her bed as she figured she could try to give her some advice. "Well, if you think that the two of you can have a relationship then why don't you tell him how you feel?"

It seemed so easy the way Asuka said it. Maybe she should just go out and tell him how she felt and see what happens. Rei got up from her mattress as she moved towards the door. "Thank you for your help Asuka." Walking out she found Shinji finishing up the dishes. "Shinji I have to tell you something."

Shinji turned to her wondering what it was that Rei had wanted to talk about. To his surprise, Rei kissed him suddenly causing his eyes to go wide with shock. Only one thought was echoing through his mind at this. ' _Is this actually happening?!'_

Once his mind started to turn back on again and confirmed this was indeed true, Rei pulled back. The surprising action of the First Child was soon topped by the next thing she said. "I wish to become mates with you."

* * *

Gendo knew he had heard the name Mari before. Yui had a friend in college with that name though with some research it turned out that it wasn't her. The Mari who was being a pilot for Eva-4 happened to be her daughter. ' _Who names their daughter after themselves?'_

At least there wasn't anything to connect her to SEELE. It seemed that they weren't lying with her being an unexpected pilot. Apparently, even the person who approved her as a pilot didn't get the memo that Unit-4 was supposed to only be used for testing didn't them in time. Still, it won't take much to demand Eva Unit-4 and it's pilot. ' _Altering the scenario with her around will be a pain but at least I have someone to throw at the Angels.'_

If she survives the engagements with them or not was of no concern to him. None of the pilots he cared much for. Rei could be replaced as they had forty clones of her. The foreigner was not his concern. As for his son, he figured whatever he did he didn't care. "I might as well tell Ritsuko about this so that we can be ready to receive Unit-4."

Getting up from his desk he walked out of his room as he saw a few of NERV personal wander around. Gendo ignored each of them before finding the woman he was hoping to see. "Doctor Akagi I have some news that you might want to hear."

Ritsuko looked up at him as she was finishing all the readings from Shinji and Rei's harmonic tests. The one thing that she was most concern about was the surprise drop at one point during the test. Ritsuko knew about each Evangelion housing the soul of someone. Part of why both Asuka and Shinji were able to synchronize with their Eva's so easily was due to them being the souls of their mother's. Rei's scores were much lower because of this fact though she suspected her ability to synchronize was instead due to something else.

Knowing what she did about how the Evangelions worked the fact that there even was such a drip was unsettling. She had wondered if it had anything to do with Yui. This would have to be put on hold as she already had several things she was going to ask them. "Let me guess the German branch decided to take back Eva-2?"

"No, apparently due to incompetence we now have a fourth pilot and Eva which will be coming here as soon as they are done." Gendo adjusted his glasses as he looked at her. He held back his anger at this change while Ritsuko was surprised to hear that they already had another pilot.

* * *

Surprisingly enough Shinji didn't faint when he heard Rei declaration. Though it did take a lot of explaining on what exactly she meant by mates. "Ah, you do know that we are kind of young to get married." Though the image of Rei in a wedding dress did enter his mind. Voice within his mind wanted to yell at him for this. "N-n-not that I wouldn't mind it."

A deep blush formed on his face at this. He couldn't believe that he had just said that. Rei, however, didn't seem all that affected by his reasoning. "Maybe for humans but I don't believe those rules would apply to us." Rei stopped wondering if she had done something wrong. "Do you not want to be in a relationship with me?"

"What?" He almost screamed at this. Shinji brought his arms up as he couldn't believe how strange and awkward this conversation had gotten. "N-n-no I just don't think we should move that far." Rei tilted her head in confusion for a bit at this. For a moment Shinji wondered how Rei didn't understand how a normal relationship went. ' _She's been caged within NERV until a year ago and her mother happens to not be human.'_

That explained why too much about everything. "Seriously, Wondergirl you go for asking him to marry you?" Asuka decided to make herself known after having watched this unfold. It took her only a second to realize what Rei was going to do and now she can say without certainty she didn't expect that. "I just thought you were going to ask him to be his girlfriend."

"But I thought I already was," The term Asuka used confused Rei greatly. "I am a girl and I believe we are friends."

Neither Asuka nor Shinji spoke as they just stared at Rei. Her reasoning was just so naive. Finally, Asuka facepalmed at this. "Verdammt!" She shouldn't have been surprised. "Of course, you don't understand," It looked like she was going to have to explain something that almost everyone her age could figure out on their own. "Girlfriend and boyfriend are terms used for two people who are in a relationship and are not married."

Rei gave an understanding nod. It seemed rather silly if you asked her but then again she didn't quite understand human courtship. Turning back to Shinji she decided to try this again. "Shinji, would you be my boyfriend?"

"S-sure." Really there wasn't any reason to not too. Weirdly enough the fact they only knew each other for only so long didn't bug him at all. Rei had a small smile at this.

"Wow, I didn't think I have ever seen anyone do something like that." The three Nephilim all turned to Misato who has a beer in her hands as she looked at the three of them. The NERV captain put the half-drunk beer down before crossing her arm. "Well, I hope I don't have to tell you both to use protection assuming you both take the plunge," She gave them a wink. "After all, I don't think Rei can have a baby and pilot her Eva at the same time."

Now Shinji wished he wasn't in the room. He didn't know if this could get any more embarrassing. "I am aware of the problems that would arise and I plan to wait until after the Angels are felt with before having a child with Shinji."

Perfect silence filled the room at this. Everyone just looked at the blue-haired girl wide-eyed. They each had the same thought wondering if she actually knew what she had just said. Asuka turned to Shinji having collected herself. "Aren't you going to say anything?"

Shinji turned to her unsure about what to say. His new girlfriend just admitted to wanting babies with him right in front of everyone in the apartment. The thing is he actually won't mind it and what was surprising him was how quick he was accepting this. "Wh-what should I say?"

That earned him a slap the back of the head. She was certain that Rei had no idea what she was even talking about. Unless she did then that just meant that not only was Shinji a pervert but so was Rei. To her, the former was far more likely. "Baka!"

"Rei you do know you are fourteen right?" Misato felt like she was too sober for this right now.

Technically Rei had no idea how old she was. Yui didn't exactly tell anyone when she began work on the clone bodies. For all, she knew she was the same age as Asuka and Shinji or she was younger. Still, physically at least she was fourteen years old and that was what she was going with. "I know but I am also biologically capable of having kids so that shouldn't be an issue."

Misato just gave up after this. She wondered what kind of irresponsible parent could have raised Rei like this. At that time deep under NERV said parent was suddenly annoyed for some unknown reason.

* * *

Asuka laid on her bed as she thought about what had happened. Rei had just gotten Shinji to become her boyfriend and was already talking about having kids with him. She placed her hand over her own stomach subconsciously. ' _Why is it that she can have children,'_ Asuka wanted to push this all aside. Why should she care that Rei wanted to be a mother? ' _It's not like I want to be one anyway!'_

Unlike any normal girl, she had never had her monthly. A fact which baffled many of the doctors until they came to the idea that she was unable to actually have kids. Asuka didn't care about it when she was told by them shrugging it off at the time. ' _Why am I having second thoughts about it now of all times!'_

" _Its because you feel like you don't have that option anymore,"_ Asuka turned her head as she looked at Rei with a glare. " _I was the same actually thinking that I couldn't have any children until mother informed me that we are in fact fertile,"_ The statement brought a confused look to Asuka face. It took her a few moments before wondering if this was, in fact, due to her being a Nephilim. " _It is."_

Rei felt a feeling of hurried joy come over Asuka. The feeling was brief but it seemed that no matter how much she wanted to deny it a part of Asuka wanted to become a mother someday. ' _Is that why you are so keen on having kids with Shinji yourself?'_

The blue-haired Nephilim looked up at the ceiling. In some ways that was part of it. Being told that she couldn't become a mother if she wanted too had hurt her. Now she could wait to become one. Almost like she had a desire to be with Shinji and have as many kids as possible. " _Asuka do you know that my mother was originally supposed to create and nurture all life on this world?"_

She did tell her about there being two lines of Angels. Adam's and Lilith's with them being the later's and the Angels they were fighting being the former. Beyond that, she didn't tell her much more than the briefest of summaries about how Lilith crashed into the planet and caused life to be born. ' _Actually, I think you might have skipped that part.'_

" _Both my mother, Lilith, and Adam are meant to go to a world and create life on it,"_ Rei closed her eyes as she showed Asuka what she had learned about the First Ancestral Race. Their real name was not translatable but the meaning was there. " _They were never supposed to both end up on the same world,"_ Rei looked down at herself before placing a hand on her stomach. " _I suspect I have inherited my mother's drive to create life and nurture it."_

The other girl didn't say a word as the information that Rei showed her was slowly processed. It would be easy to misinterpret Lilith and Adam as terraforming tools if one didn't know everything. In truth, they were the peak of what the First Ancestral Race could do. In many ways, both Adam and Lilith were made from them and imbued with more than enough knowledge and powers to very easily be seen as Gods. ' _What would happen when it's over?'_ Asuka question caused Rei to look at her. ' _When we win and when your mother gets free what happens then?'_

" _Mom would likely use her powers to undo what damage she can and if they want would teach the world all she knew,"_ Though she was unsure if her mother would even do the later. SEELE, NERV, Adam the three of them had scared the world each in different ways. Perhaps, in the end, Lilith would just fix the damage Second Impact caused and allow humanity their own future. " _We'll be free to do whatever we want afterwards."_

A nice thought to know that there wasn't anything that Lilith would demand of her. Speaking of which Asuka wondered what Rei wanted to do with her life. ' _Let me guess you going to become a mother and have a nice quiet life?'_

Such a thought hadn't crossed her mind. Thinking about it Rei did have to admit that the idea of simply having a rather normal life made her happy. Perhaps that was something she would very much like to have when the war was over.

* * *

In the next room, Shinji was tossing a bit in his sleep. Within his dream, he was on his own sitting on a chair with the only light shining on him. "Hello?" He got up from the chair looking around as he saw nothing. He tried to sit back down only for the chair to have disappeared causing him to land on his butt. "Well, that sucks."

Getting back up he was met with himself. Himself without his current eye and hair colors. The mirror of him was staring at him appearing like how he would be without his changes. "Who are you?"

He was about to answer that when he saw another figure. This one covered in a clock of darkness with two glowing eyes that were like his own staring back at him. The figured walked to the side of his mirror self. "Are you a Human?"

"Are you an Angel?"The two of them stared right at him as Shinji looked at the both of them. Out the concern of his eyes, he saw something. Turning his head he was greeted with both of them again.

He did this again and again until he was surrounded by the both of them. Shinji started to feel rather claustrophobic as they were all looking at him with unblinking eyes. They spoke in perfect harmony. "What you?" They took a step closer to him. "Angel or Human?"

They continued to get close as Shinji found himself trapped. As they continued to push into him. He closed his eyes before opening as he saw himself looking around again. He spied his mother on the phone with someone. "Listen here I want to make one thing absolutely clear if we can't get a test subject for Eva-2 then have Kyoko do it."

Yui ended the call as she punched the wall in frustration. Shinji blinked as he realized that this had to be a memory of when he was younger. "I need to see how the Evangelion acts without a soul for my plans to work." Yui turned her head over as she saw Shinji. She put on a smile that sort of creeped him out. "Deary how much of that did you hear?"

"What's an Evangelion?" Young Shinji's voice was heard coming out of his mouth. Yui's expression didn't change as she pulled out a bottle for him.

A feeling of fear came over him as Yui handed him the drink. "Here why don't you drink some milk and I'll tell you."

His younger self-took it and after taking a gulp of it started to feel rather heavy. "Mommy I don't feel so good."

As he looked at her with a kind yet creepy smile on her face he lost himself to unconsciousness. The sound of Yui's voice being the last conscious thing he remembered. "That's good to know now sleep and forget all about it."

Shinji awoke staring at the ceiling as the Sun's light started to pierce into the room. He brought his hand up to his head as he felt a minor headache coming on. ' _What was that all about?'_ Did his mother really do that to him? ' _Was it really a memory or was it just a dream.'_

A part of him hoped that it was the later. The former just seemed so unlike his mother. Drugging him because he overheard something about the Evangelions? He didn't know what his mother did before her death but he was certain that this working on the Evangelions wasn't the case. ' _Why do I feel like I am lying to myself?'_

The sound of knocking on his door caught his attention. Well, more of pounding at it if he was being honest. "Hey, Boy Wonder you know it's almost time for breakfast!"

"Coming," He got out of bed in his pajamas as he opened the door finding Asuka eating a bit of raw bacon. Actually, now that he wondered if she had to eat raw meat did that include other animal products? ' _I shouldn't really ask that.'_

Asuka swallowed the meat with her mouth. "I think Rei cooking you and Misato breakfast also," She pulled out of her pocket a card with his name on it. "I forgot to give this to you yesterday it's your NERV ID card Doctor Akagi wanted me to hand this to you."

Shinji took it as he looked at the picture on it. Taken just before he headed to Tokyo-3. Just before he ended up drafted into a war. At the very least he knew that these worked as credit cards and as he found out from Misato he did get paid for doing this. It still, didn't make up for the fact that he was effectively forced into a war though.

* * *

Gendo looked at the timer that was set in his office. It counted down to when the next Angel was scheduled to attack according to the scenario. Eva-2 would be here just before the Angel was yo arrive though before they could get it fully ready for combat according to the current timetable. ' _It seems that Eva-1 will have to be used yet again.'_

At that moment the door opened up to his office as Kozo walked in. "Well, I just overheard Captain Katsuragi talking over with Doctor Akagi about something surprising it seems that Rei and your son have started a relationship."

Gendo was mildly surprised to hear this. There was a bit of disgust at this though he supposed if Ritsuko was to be believed Rei DNA was barely any bit related to his son now. Whatever the case if his son wanted to have a relationship with a clone half Angels made by his late mother in her image then so be it. ' _You know if he gets a bit too confident I can just tell him about it and he'll be crushed again.'_ For a moment he felt like something was trying to silently burn a hole through the back of his head in anger. ' _Must be nothing.'_

" _I. AM. GOING. TO. END. YOU!"_ Once again the fact that Lilith was weakened and held down was the only reason Gendo was a bloody splat on the floor.

* * *

 **Rei is with Shinji first but don't worry Asuka will be joining them later on. Just in case anyone gets afraid or made hat Rei got with Shinji first. I lead in with Rei and I'm sticking to it ok. I should shut up now about this.**

 **Cya all next chapter.**


	7. Chapter 6

**Well, this took a bit longer than I would have liked. I did make it longer as a trade-off though. Hope you like it.**

 **Thank you Scattershot98 and Hellsink Bathhall for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Lilith's A.T. field hummed over the Evangelion Unit that had been brought in. Touching Eva-2 she was able to get an idea on what it looked like both inside and out. Reaching in deeper she made contact with the soul that had been forced into it. " _Wait are there two souls?"_

Taking another look it turned out that it wasn't two souls. It was one soul that had been split into two. Lilith could feel the pain and insanity from each half of them. Unlike her, the effect of splitting up the soul of a human would drive them insane. They couldn't eventually regenerate from it like she could. " _Who is there?"_

The two voices that Lilith heard from each half of the soul was just unnatural. Before the two half of the soul appeared taking on the form of what Asuka and Shinji had seen her as. " _I mean you no threat."_

The two halves of the soul before her did look like Asuka somewhat. It was obvious that it was her late mother. Her insanity brought about due to losing half of her soul to the Evangelion. Then at death, they decided to put the other half in. " _Are you an Angel?"_

" _Yes, I am Lilith,"_ As soon as she said that the two halves of the same soul recoiled from her in fear. Lilith wasn't surprised by this. She reached out to the two of them as they tried to get away from her. On contact, Lilith showed them everything. After a few moments, Lilith pulled back as they looked at her. " _I'm so sorry for everything."_

The two halves of Kyoko looked at the Angel in front of them. They had noticed the change in their daughter for a long time. Neither could figure out why that was. Until know that they had just seen Lilith alter her in hopes of preventing the plans of SEELE from coming true. " _I understand."_

Lilith looked at the two of them before reaching out again. They didn't deserve to be this broken. Taking both parts of them she pulled them close as their natural A.T. fields recognized each other. Before either of them knew it they were whole again as Kyoko blinked in surprise as the spiritual incarnation of Lilith. " _There I think you are much better whole then apart don't you think?"_

Kyoko took a moment to make sure that this had actually happened. Ever since she was told to test out the Evangelion that she helped designed she felt herself be split into two. After her other half killed herself in an attempt to end the suffering she couldn't seem to pull herself together. " _I'm me again."_

Lilith had a smile before she pulled back. She couldn't stay within the Evangelion for long. Especially one being monitored like this. " _I have to go now we'll talk later ok."_

Kyoko gave Lilith a nod as the ancient being pulled A.T. field back from the Evangelion. As she did she moved around and saw Ritsuko looking over a blood sample that she managed to talk the German branch into giving to her. Lilith hovered around her as Ritsuko's eyes went wide. She had compared her sample to a normal girl her and found numerous mutations and genetic anomalies. Anomalies that were present in only one other person she knew. ' _The Second Child is like Rei!?'_

Lilith reached in as she readied herself to overtake her. She was still unsure on where her loyalties ultimately laid. At first, Ritsuko thought that she should go to the Commander about this. Lilith was about to push out control of her body when Ritsuko surprised her. She dismissed that thought immediately after having it. ' _Why am I even thinking of letting him know anyway?'_

Lilith could see that she had grown disinterested him Gendo for years now. There was a lot of things she had done to get him to notice her and all he could think about was his late wife. Ritsuko put in a few commands and soon the computer deleted the results leaving not a trace in the network. As she turned away from the keyboard she felt a presence in the back of her mind. " _Thank you."_ Ritsuko turned around as she found no one there.

* * *

It had been a week and still, Shinji's relationship with Rei was the talk of the school. Some wondered how this came to be. A few rumors sprang up. One was that they were childhood sweethearts, another told that it was due to them both taking part in the same organization, and the more outlandish even thought they were related. Then when Asuka came to school with her weirdness another rumor popped up.

When Asuka tracked them down that rumor quickly died away. More out of fear for the foreign girl then anyone actually thinking it was real. ' _Really the three of us in a relationship?'_

The image of such a thing did cross his teenage mind though he pushed it away as quickly as he thought of it. Realistically that sort of teenage boy's wet dream would never happen. "Hey, Boy Wonder," Shinji looked up as Asuka turned around to see him. "You noticed that Rei only really has her school uniform?"

That was something he had noticed after a few days actually. He didn't want to bring it up because he didn't think it was his place too. "You need to take her out and get her something else to wear."

"Why me?" Seriously, she just out of the blue brought it up and was telling him to do it. Asuka rolled her eyes at this.

"What are you stupid?" Asuka rolled her eyes in annoyance. Although given how anti-social both him and Rei were she wasn't surprised. "You are her boyfriend so take her to the mall to get something besides just her school uniform to wear."

That was a rather solid argument actually. Two choose this time to speak up having overheard the conversation. "I never really thought about wearing other outfits before nor have I gone to the mall," Rei paused as she thought about what she had heard from several classmates. "I believe that couples occasionally go to the mall on dates correct?"

Shinji had a light blush on his face at this. He had never thought he would be going on a date before. Especially not with a cute girl like Rei. ' _I didn't think I would be fighting a war with a giant robot while also being the thing I am fighting.'_ The bell was heard as class finally came to an end. Shinji got up and turned to Rei. "I guess we might as well get you something else to wear so you don't have to reuse the same thing all the time."

Rei gave him a nod as the two of them walked out. The light blue haired girl took his hand with her own. A faint blush formed on Shinji's face s the two of them walked out of the room together. Asuka looking at the both of them couldn't help but roll her eyes. ' _I mean they do look cute together.,'_ She paused as she felt a tinge of jealousy for some reason, ' _Why am I feeling this?'_

* * *

When it awoke it saw the creations of the current inhabitants. The children of another progenitor. Confusion was the first thought in its mind at this. Wasn't the planet supposed to be for them? It looked up at the system's star overhead wondering if they had actually been blown off course.

It didn't remember much but it did know that it had to find its progenitor. With any luck, they could tell it how to proceed. Reaching out with its instincts its A.T. field shot in all directs before locating what it was looking for. A progenitor signal on a bunch of large nearby islands. It couldn't tell if it was either it's own or these things progenitor. If it was the later then it had to try either to ignore them or kill them. The former would mean it had to mix in with them and trigger a reset of the world with its power.

Floating out of the hole in the wilds where it had been resting the spawn of Adam moved for Tokyo-3. It moved to find Adam unaware that the progenitor it was following was in fact, Lilith.

* * *

Shopping for Rei was a bit of a problem as Shinji soon learned. The girl had never really had a style nor did she have an idea on what she wanted to wear. The first thing that came to his mind was to ask her favorite color. "I don't have one aren't they all just colors?"

He really shouldn't be surprised by how many human concepts seemed alien to her. Her only parent was an ancient god-like entity which crashed into the planet and been in a coma for four billion years. Lilith likely had a poor understanding of human customs herself. "I mean it would help us figure out what to get you if we knew what color you liked them to be."

It seemed rather weird that her outfit had to have colors that she liked. Rei only understood the need for clothing as a form of minor protection, thermal regulation, and a sort of ingrained tradition among humans to wear them when in company with each other. If she could Rei likely would just walk around in the nude. "Very well," Rei tried to picture what colors she found suitable. The first thing to come to mind was the shade of blue that her hair was and simple white. "I believe blue like my hair and white are my choice."

Finding an outfit with such colors was going to be a tough challenge. Still, with at least some idea on what to get her, both Shinji and Rei started wandering around the stores. Money wasn't an issue due to Rei barely ever spending any herself outside what was necessary for a Nephilim such as herself. Because of this, they could ignore the prices as they searched the various stores at the mall. As they looked around for outfits for her Rei's eyes caught sight of a store with a strange symbol that was here within the clothing section of the mall. "Shinji, do you know what that store sells?"

Shinji turned and blushed as he knew exactly what kind of stuff that store sold. "It's not a place for us."

"Why not?" Rei could read the tagline on the shop. It said it was a place for couples to buy things for a fun time. Wouldn't that be something that they should look into?

After an awkward moment, Shinji looked at all of the people around them. He blushed before pulling her close and whispered into her ear about why they couldn't. Rei gave him a nod in understanding. Shinji had a mental sigh of relief at this. "C-come on let's try out another store."

Just before they could Rei stopped and looked up. She felt the presence of an Angel of Adam coming. Before they know it the building rumbled as parts of the ceiling started to break up. The emergency alarm sounded barring. "An Angel is attacking we have to get back to NERV."

Above both of them, the ceiling surprisingly gave out. Rei acted immediately and pulled Shinji to her as the rubble fell on the both of them. Shinji opened his eyes expecting them to be crushed only to see a glowing orange barrier blocking the rubble from hitting them. "What the?"

He remembered it was an A.T. field. Rei was a awaken Nephilim and as such she had an A.T field like any Angel and could use it to protect herself, or in this instance it was both her and Shinji. As soon as Rei was sure that the impacts stopped she looked at Shinji. "We should dig ourselves out of here."

Shinji looked at the rubble around them. That may take a while even with their super strength. That meant that Asuka was likely going to have to face the Angel on her own until they could get out. ' _She did keep bragging that she could do this on her own.'_ A small part of him was worried that she would be in trouble without them. ' _There no need to worry Asuka been doing this longer than the both of us._

* * *

Gendo looked on as the Angel began to rampage across the city. He frowned as he wondered were Shinji and Rei were. Misato came in with Asuka following behind her. The Commander of NERV turned to Misato noticing that neither Rei or Shinji were with her. "Captain Katsuragi where are my son and the First Child?"

Misato turned her head over to Asuka. She had already asked the German pilot about that and learned that the two of them had decided to head for the mall to get Rei more clothes to wear. "They've been delayed because of a date sir."

The Commander mentally cursed at this. Just what he needed two of the children's relationship getting in his way. At first, he wanted to break them up but figured that it was unavoidable regardless. After all, unless he kept them within NERV there was always the risk of being late when an Angel showed up. "Fine, Doctor Akagi get Eva-2 ready for launch."

"But sir we are still getting the Eva properly set up," They had moved some of the equipment that the Evangelion came with into the proper caches and storage but the big problem was the power cable. The German branch was using one that wasn't properly adapted for their systems here at NERV's main branch.

Gendo didn't care one bit about the problems. If they waited too long then the Angell would begin digging into the Geofront. If that happened it would attack them Eva-1 and Yui. He couldn't let that happen. "We don't have any options and the longer we wait the more people we put at risk!"

His words brought an end to any argument. As much as Doctor Akagi wanted to protest the decision, the Angel was just too much of a threat. They didn't have much of a choice in what they could do. "Fine, I'll get Eva-2 as ready as I can."

With that done, Gendo turned his gaze to Asuka. "Suit up and get ready for your first taste of battle."

She gave him a nod and turned around to get suited up. For a moment she recalled Rei's warning. Call it a hunch but Asuka figure that he didn't actually care about the Angel causing deaths. As she left she turned her head ever slightly as Gendo returned to look at the video feed of the Angel.

* * *

Asuka stood out as Eva-2 was readied for launch against the Angel. She felt a presence around her for a brief moment. She knew it was Lilith thanks to the contact that Rei had shared with her. She brushed around looking for each of the kids and only found Asuka. The redhead didn't know if she was wishing her good luck or something else. Whatever the cause the young Nephilim had a job to do. ' _Alright, my first fight with an Angel.'_

A part of her wondered were both Rei and Shinji were. The two of them did say they were going to the mall to get Rei dome clothes. They had either been running late or got caught in the panicking of civilian evaluations. Up in the control room, Ritsuko turned to Gendo. "Sir Are you sure we shouldn't wait for the First and Third Children?"

"I'm certain by the time they got here thousands would already be dead," Inwardly he wanted to see just how good the Second Child actually was as a pilot. For someone who had been practicing to be a pilot since she was young, she had nothing besides the usual piloting simulations. He watched as Asuka was finally in Eva-2 has they readied the Eva for launch. ' _Let me see just how good you really are.'_

The LCL fluid flooded her cockpit as Asuka opened her mouth. The redhead could smell the scent of blood around her and on reflex, she drank some of the LCL fluid. The strangeness of her action wasn't known to anyone watching. "All systems clear synchronization rate stable at fifty-five percent."

The clamps holding Eva-2 released as the hatch leading up opened. "Eva-2 ready for launch!"

Eva-2 was rocketed upwards before appeared into the battlefield of a city. Asuka didn't need much in the way of help to get the feel of her Eva. Compared to Shinji who was forced to learn in the fight Asuka had trained enough to understand how she moved in relation to her Eva. "Alright, Asuka two blocks ahead is a weapons cache."

Asuka within her Eva gave her a nod as she headed for the of weapons. Opening it she looked at them as one of them caught her attention. She had hoped that it had come along with her to Japan. It was something the head engineer in the German branch had made for her after watching her train with her Progressive knife. She pulled up the sword and removed it from its scabbard.

The sword was made to appear like a medieval longsword built in a vein of the Progressive knife. Out of all the things she's trained with this was the one she put the most time into. It was made for her after all.

* * *

The Angel turned as it had felt a strange signature. When it had entered the city it felt the feeling of another Angel. This one wasn't like it though. From the feeling, it had this Angel belonged to the other Progenitor. It was nearly the spitting image of its parent. In fact, it had almost mistaken it for the other Progenitor.

The Angel turned its attention to a newcomer. The red giant with had a sword in its hands. For a moment it actually thought it was one of its kind. It greeted the giant wondering if it knew if their progenitor was here and what had happened. As Eva-2 came at it with the sword raised it realized that this wasn't one of its own kind. The A.T. field flared into being as it blocked the swing of the large swords. Outside two parts of its sides whipped formed powered by its A.T. field and counter-attacked.

Asuka immediately brought the blade up to counter the hits. Before charging back again slashing at the A.T. field and even forcing it back. The Angel decided on a different approach moving back while looking at the nearby building. With a mighty swing, it broke its middle floors had the top of the building came down at Eva-2. Asuka reacted at this as Eva-2 jumped out of the way while the Angel used this opportunity to move back and think up a new plan of attack.

Asuka wasn't going to let them have the chance. She charged forward, yelling as she did before bringing the sword across what passed for a chest on the Angel. "Don't think that a building would slow me down!"

The Angel responded by sending out its whips and launching on to the handle of the blade within her grasp. The two of them started to struggle at this as the Angel tried to remove the sword from her grip while Eva-2 fought to pull the Angel down. The ground below the Eva started to break as it dug its feet into it.

Unknown to the both of them Rei and Shinji hardware seeing the two titans fight for control in the middle of Tokyo-3. Shinji looked out at the tug of war between the two seemingly evenly matched opponents. Rei, however, knew that Asuka was making a foolish decision. "She's letting the Angel recuperate its A.T. field she should abandon her weapon before," No sooner as those words left her mouth did the sword go flying up by the A.T. field pushing both of them back. The edge came down and cut into the umbilical cable slicing right through it. "That happens."

* * *

With Eva-2 cord cut the eternal power batteries were active to allow the Eva to continue to fight. Even then it wasn't going to last long and Asuka knew that this was going to be a huge problem. What's worse as the Angel had managed to disarm her and both Shinji and Rei were still, nowhere to help her. ' _Great my first combat mission and I'm losing.'_ She had trained her whole life for this and she was about to be put down due to a technical problem. ' _Verdammt, I can let it end here!'_

As Eva-2 stood its ground the Angel turned to it confident in its victory. It knew that something was wrong with this false Angel that these children of the other progenitor had made. It raised up its whips as it ready to attack. At that moment Asuka heard a voice speak to her in the back of her mind. ' _Asuka,'_ Asuka paused time seemingly slowing down. ' _I'm sorry for what I did.'_

"Mama," A single tear left out the corner of her eyes. As the two whips came down Eva-2 caught them both. Back in the NERV headquarters, Asuka's synchronization rate shot up rapidly. Finally, it hit eighty as Asuka glared her teeth out and brought to bare. "Ich werde dir den phallischen Kopf abreißen!"

At that, a surge of energy was felt pulsing through Asuka. Like someone had broken invisible chains holding her back. With a primal roar two red wings of light, each one shaped like some kind of talon-like limbs, shout out from behind her. Asuka had awakened her Angelic powers. A savage smirk filled her face as Eva-2 let out a roar as its hidden mouth opened entering a Berserker state. With a mighty pull, Eva-2 pulled the Angel off the ground and into the nearby buildings.

The Angel turned to the Evangelion as it could sense just what was piloting it. Within the false Angel was a true one. An Angel derived not from its parent but from Lilith. Eva-2 launched itself as it brought itself it's firsts down the Angel. It's A.T. field barely stopping it but in the end, it didn't matter.

While the video feed continued though it constantly glitching out showing Eva-2 starting to brutal smash, even rip off bits of the Angel with them unable to tell how the real problem that the Command Center faced was that all attempts to communicate with the pilot had failed. Ritsuko looked at the data in front of her. "This doesn't make any sense the MAGI system keeps picking up that another Angel just appeared next to them!"

Unknown to either of them Lilith had begun to run interference through the system. The MAGI system was one thing Lilith had discovered she could alter due to parts of the computer systems unknowingly interfacing with her Seed-ships systems. " _Come on Asuka you can do it rip it part."_

From the readings, Eva-2 was almost out of power. A state which Asuka was likely to know herself. On the screen the Eva pulled out its Progressive knife raising its hand up it slammed it with all its might into the Angel. The creature screamed as the blade pierced into its core. At that moment power was lost to Eva-2 as it fell over.

Within the Eva, Asuka felt herself losing consciousness. Just before her eyes closed she thought she saw her mother looking at her with a smile on her face. ' _Mama…'_

* * *

Rei looked at the unconsciousness Asuka as she reached out with her A.T. field to confirm what she was told. Asuka had indeed awakened her Angelic powers during the fight with the Fourth Angel. She pulled back as Asuka's eyes opened being greeted with the white ceiling of the medical ward. "Where am I?"

"The medical ward after you destroyed the Angel NERV retrieved Eva Unit-2 and found you unconscious," Rei answered as she looked at her fellow Nephilim in the eyes. "I remember that this happened to me when I awakened."

At hearing that Asuka shot up. Taking a moment she felt a strange sensation. Like she was more alive. Like a weight holding her down had been lifted. "You mean?" She received a nod from Rei as Asuka felt excitement well up within her. ' _I killed the Angel and I managed to awaken at the same time.'_

Her mood was soon brought down as she realized she had no idea how to use her newly awakened abilities. A panic set in at the thought of accidentally showing her wings off with people seeing. Especially, if she did so when at NERV. " _No need to worry I will teach you how to control your abilities remember."_

She turned to Rei as she remembered that. While she was in that rage like state something happened. Her robot had formed a mouth and through it, she had felt the taste of the flesh of the Angel. It was just far too life-like for it to be simple simulations. A thought crossed her mind that made her rather uncomfortable. "Are the Evangelions actually alive?"

The room turned deathly quiet as Rei looked at her. It was all the proof that Asuka needed to know. Knowing that it couldn't be hidden Rei answered. "Yes, the skeleton of each Evangelion is made from an organic body using the flesh of an Angel," Rei had seen them dispose of one of the Evangelions that failed to form once. Her mother told her that they had a whole graveyard of such things within NERV. "All current working Eva's except for Eva-1 are made with the flesh of Adam."

"What's Eva-1 made with?" Asuka was feeling disgusted at this. They were practically making her pilot living thing without even telling her. As soon as she thought about it she realized that there was one other Angel that they could use. "It's made from your mother's flesh isn't it?"

Rei gave her a nod in confirmation. The albino was just disgusted by the fact that her mother was literally helpless on the chance that Gendo wanted to make more Evangelions from her. Although that paled in comparison to the creature that was using it as a new body to inhabit. "Yes, mother originally thought that they had no other option and was willing to let them cannibalize her in order to fight Adam's spawn."

Asuka sighed and laid down. She got that something terrible and rotten was within the core of NERV. A reason that made Lilith reconsider this and go with a new plan. "Does Shinji know?" Rei shook her head. "Why not?"

"Because he hasn't asked."

* * *

He rewatched the recording of the fight that SEELE was given. At first, it seemed that Eva-2 was on par thanks to its pilot's training. Then its cable snapped due to how quick they had to hastily put it together. That seemed to be the end to that. Then the feed became clouded by glitches as Eva-2 began to assault the Angel tearing into it. "Well, that has to be an embarrassing way to be defeated."

Kaworu turned off the video as he laid down. He looked up at the ceiling wondering what he should do. The Nephilim of Adam knew about SEELE's rather stupid plans. It seemed they had a terrible understanding of what the Dead Sea Scrolls actually talked about. Regardless he knew that this war was between both Lilith and Adam with SEELE moving to take advantage of it. ' _That's just the way it is we can't exist on a world with Lilith's creations.'_

Personally, he would feel a bit bad at wiping out the current tenants of the world. There culture and media was kind of nice and their food a bit of a treat. "You know I might just pay the pilots a visit."

* * *

 **Asuka gets her first kill and also now she has awakened. As for her wings I was basing them on Sarah Kerrigan Queen of Blades wings from starcraft in terms of shape (though obviously red wings of light.). Now Shinji just needs to do it as well. You know I am surprisingly enough having the most fun writing Lilith and Rei in this story. I don't know why but it just feels so good writing their interactions. Anyway, before we leave off you want me to give Rei and Asuka Angel names? I thought about it but I want to hear your thoughts.**

 **Cy a next time.**


	8. Chapter 7

**Another update so soon after the last. Surprisingly I'm on a bit of a roll. Sorry, for its smaller size by the way.**

 **Thank you Scattershot98, Hellsink Bathhall, and Guest for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Ritsuko looked around at the tank as the floating clones of Rei just stared at her each one as creepy as the last. She rarely came down here more than needed and even then she tried to find a way to stay out of here. When she found out the truth of this place and why Rei exists the whole place became unsettling. Like a temple to the mind of a mad scientist. ' _I need to check something though.'_

When she saw the similarities in Asuka's DNA to Rei she had several theories on why that was. Her first was that Asuka was something of a clone herself. Yui had several scientists that she worked with closely and given how she was it wouldn't be impossible to see them being like her. One of them did name their daughter after themselves after all.

Looking into Kyoko, the mother if Asuka, brought up some questions about that. For one she didn't have any narcissistic tendencies. She even seemed generally humble from the psychiatric reports that she had on her. Everything didn't add up until one thing. Her husband leaving her.

Kyoko was mad that he had done such a thing and even fell into depression a bit. The next part of the reports she had was that she had gone to a sperm bank. Apparently, she had hoped to become a mother and with her husband home, she had to pick another option. Ritsuko at first thought that it was a cover story for the fact that Asuka like Rei was secretly an artificially made person.

At least until she found the medical reports. Removing a sample of Rei Four's DNA the doctor turned to make her leave. ' _Kyoko was pregnant for nine months before giving birth to Asuka,'_ That ruled out her being genetically engineered as Asuka's daughter. ' _If it's true as the report claims then she should be human so why is it that she and Rei share the genetic markers of an Angel?'_

The voice from before echoed in her mind. A thank you from someone who wasn't there. Call her crazy but she felt like something might be watching her. Perhaps she was crazy as the idea that she had seemed to be just out there. ' _I do need answers though.'_

* * *

Asuka and Shinji stood out in the junkyard that Rei had led them too. The sun outside seemed to be setting overhead as Rei turned to Asuka. She spread her own A.T. field out to make sure that no one was around from Section 2. "This is where we will begin its isolated enough that we shouldn't be found out."

"Wait, if this is where you are going to train Asuka why am here?" Shinji spoke up as both Asuka and Rei turned to him. The German pilot had wondered why assuming that Rei just wanted her boyfriend to come with them.

"It would make your training easier if you watch Asuka," Rei explained to him. She had already thought about this when Asuka had awakened her powers. "This way you would be able to know what to do when that time comes."

That did make a lot of sense. Rei wouldn't need to repeat the same thing over again and Shinji could quickly jump into lessons after a small time to get acquainted with his powers. Taking a seat on top of an old car he watched as Asuka began her first lesson. "Now first we should start simple try calling up your wings."

Asuka was about to answer that she had no idea when she stopped herself. To her surprise, she realized that she did know how to do that. Out her back her two red wings of light appeared much to her surprise. "Ok, how did I just do that?" She paused before looking at her wings. "They look more like talons."

"It's something you instinctively know how to do," Rei explained before her wings shot out of her back. It was an example as Asuka looked at her. "As for its appearance your wings reflect your soul as an Angel," It was what her mother had told her about the similarities in her wings. Rei was extremely close to her mother and calling her a clone would be correct both literally and metaphysically. Yet, even as a clone, she was different from the original. "Now I think our next test is for you to use your A.T. field."

Asuka gave a nod as Shinji continued to watch from the sidelines. Both of the girls' wings disappeared as they continued with the next part of their training. As he paid attention he started to wonder about his awakening. The dreams question echoing in his mind. ' _Are you a human or an Angel?'_

* * *

Gendo looked on as he stood in front of Lilith. It was, of course, that time again to stand before the body of one her and speak his thoughts. For a moment he thought about the relationship that Rei had gotten into with Shinji. "You know I wonder how my son would feel if he learned just what he was really dating."

Lilith wanted to see if it was possible to drown him in LCL. She knew what he was picturing. His son being horrified and broken by the thought of being in a relationship with what was effectively his half-sister. " _For a man who loves his mate enough to risk the world you care nothing for the child you both spawn nor the girl made in her image."_

"Perhaps I could get them married to make the issue even worse for him," In the wake of Second Impact marriage laws were relaxed. Technically the laws were not changed back even after the fear had died down. "I think I should order Rei to marry him."

The ancient being would roll her eyes at this. He still thought that Rei was under his control. A girl he hoped to turn into a suicidal nihilist devoid of any wants or desires. Once that was the case but after Lilith contacted her daughter she slowly moved her away from that. Lilith could see within her a desire to live when this was all over and that alone made her happy for her. If only she didn't have to play the part of listening to him. " _When the time comes Gendo you would find out that my little girl hasn't listened or cared for you in over three years."_

Perhaps that combined with the revelation of his wife caring nothing for him would be better than killing him. Learning that all he tried to accomplish was, in the end, pointless would crash him. A gate worse than death though given her powers she could probably still kill him, and make him live with that knowledge. The perks of being a god-like entity. "Though I do wonder how you would take the revelation of being married to someone if you were aware of it."

For once Gendo actually posed a rather thoughtful question. The Commander of NERV turned to leave. SEELE was going to be calling him soon. Lilith looked on at him as she reached out again. As much as she wanted to think about his questioning Lilith didn't care to waste time with it. Her A.T. field passed over the Eva cages as it looked at each of them. Eva-1 was closed off to her. Yui was likely aware of her and was blocking her off. Eva-2 was welcoming to her and while she wanted to talk to Kyoko she had someone else she wanted to speak too.

Moving to Eva-0 Lilith entered her A.T. field into it. She waited until the soul within it to acknowledge her presence. " _It's been awhile Lilith,"_ The soul within the Eva had her back turned to her before turning around revealing Naoko Akagi. " _What brings you to me this time?"_

The former scientist of NERV's predecessor organization GEHIRN had been forced into the Eva soon after her death. Lilith had wondered who was within Eva-0 after her daughter's awakening. As each Eva had to have a soul to function even if her daughter didn't need the soul of her parent to pilot the Eva. When she did she found her in a dream-like state before waking her up. " _Your daughter has found out that Rei is not the only Nephilim."_

Maoko crossed her arms as she looked at the projection if Lilith. The woman knew everything. The reason for Second Impact, SEELE's plans for immortality, and even the twisted nature of Yui. It didn't take much more for Lilith to ask her to help fight them. " _Let me guess she was going to go to Gendo with it and you had to overtake her?"_

Lilith shook her head. " _No, she chose instead to delete the results and keep it to herself,"_ She knew Ritsuko was going to compare Rei's DNA to the clones within the tank. When she did she would be aware that she wasn't as Gendo and Yui had believed her to be. " _I think I should contact her and see if I can get her to help us out."_

" _And you came to me about this because?"_ Maoko didn't know how this concerned her honestly.

" _Because you are her mother and I figured you deserved to know,"_ Lilith knew how poor their relationship was. Regardless she knew that it wasn't beyond saving and that in the end they really did love each other. She could see into their souls after all.

* * *

Ritsuko was surprised by the result she had gotten. Rei Two was different from Rei Four. On a genetic scale, it was small but noticeable. Rei Two was genetically stable and if she suspected was able to function perfectly fine. Compared to the rest of the tank clones who were genetically unstable and had to rely on LCL bath and special medicine to stay alive. ' _She doesn't need either of this though.'_

If anything all it did was just temporary boost her likely accelerated healing factor. A factor she possessed due to being what she was. "Is this just a fluke?"

Ritsuko shook her head at this. Yui wasn't dumb enough to have one of the clones be perfect genetically. They each had the same purpose after all. Someone had to have altered one of the clones while in development. ' _Or something.'_

Thinking about it the level of skill it took in genetic engineering to fix all these problems was far beyond even the most talented of scientists within the field today. That left the only option being someone who wasn't human. Looking at her NERV card Ritsuko remembered the one time Gendo took her down to see the body of Lilith.

The Angel they found within the Geofront. Rei soul was supposed to have come from it. There own Angel under their control. ' _Could it be?'_

She took her card and raced out if her room. There were only three people in NERV with the clearance to go down to that level and she was one of them. As she boarded the elevator her mind raced on what she was going to do and what she was going to say to the giant in the basement. Finally, it reached the level as Ritsuko walked out and was soon in the presence of Lilith.

Looking at the crucified Angel Ritsuko stole herself. The rational part of her brain told her that this was crazy. ' _Maybe I am going insane?'_

" _I won't say that,"_ Ritsuko's eyes widened as a figure appeared before her looking almost like an older Rei with noticeable differences. " _You are actually quite sane when compared to at least half the people who have ever worked here."_

She knew who this individual was. It was Lilith the being whose soul was supposed to rest within Rei. Her crazy theory was looking a lot less crazy. "Y-you're actually here?" She paused before speaking again. "Who is in Rei?"

Lilith giggled at this. Sure, Ritsuko was having a nervous breakdown but Lilith just found the question so silly. " _My daughter Rei is within herself,"_ Lilith placed her nonexistent hand of Ritsuko shoulder as the woman felt herself start to calm down. " _Here can't have your emotions go wild because trust me you will have plenty of that for later."_

In just under half an hour Ritsuko was starting to regret her career choices. Lilith had explained much of what was going in. First, she talked about why the Angels were here. Simply put they been here ever since both she and Adam ended up on the primordial world that was earth billions of years ago. Add to that Lilith was the source of all life on the planet not related to Adam thanks to her blood, the LCL, mixing with the newly formed seas in the ancient world. Oh, and the impact that created the moon was also her ships doing.

The ship that NERV was formed partly inside and that she had been in a coma when GEHIRN found her. Lilith then went on about what she had done to the three pilots. Ritsuko wasn't as surprised as she should be to discover that Shinji was also a Nephilim like Asuka and Rei. "So you fixed up one of Rei's clones, turned both the Second and Third child into your own Angels so that they could fight Adam's?"

" _That is only part of it,"_ Lilith was worried about Yui and even about SEELE. Gendo was far easier to manipulate and understand given how much time he spent close to her. Yui had found a way to close herself off and SEELE were too far away for her to touch and learn their plans. " _You know of the Commander's plans correct?"_

She had indeed seen most of it though the end goal was still unknown to her. Looking at Lilith she was starting to think that it wasn't as good as she thought. "You know what he is planning don't you?"

It wasn't much of a question. Lilith gave her a nod before looking down. " _Both he and his bosses are planning to perform_ _Instrumentality, merging everyone's souls together, or if you are me and_ _ **know**_ _the language of the First Ancestral Race, effectively trigger the terraforming equipment fail-safe programs on my Seed-ship."_

If there wasn't a huge threat brought on by their actions Lilith would laugh at this. The Dead Sea Scrolls that they had was likely a poorly translated records from both her Seed-ships workings and perhaps even a surface scan report from before it crashed into the earth. SEELE seemed to think it was a method to grant them Godhood. Lilith knew it was a way for her to save her creations on the off chance they hadn't reached a level to protect themselves from a danger that threatened all life on the planet.

Of course, if she wasn't in a coma she would have long since taught them about that. That and they wouldn't have been able too with her around. " _I made the three of them the way they are now in order to prevent such a plan from ever coming to be, and so far it seems to be working."_

"How?" Ritsuko questioned wondering just why those three pilots were so important. Rei she could get as she was supposed to be the means to cause whatever plan both Gendo and SEELE were wanting.

Lilith gave her a mischievous smile. The kind of mischievousness one had when you are going to literally destroy the desires of a bunch power hungry psychopaths and there was literally nothing they could do to stop you. " _Oh, you know by having three of them get together as powerful Nephilim who I have control over the Seed-ship too,"_ The former was more of a happy accident but she could honestly see the seeds of a three-way relationship forming between them. A little push here and there and she'll have the start of a new species. " _Rei already knows everything and with her, the other two can easily avoid any manipulation by them or better yet turn it in a way to screw them over."_

* * *

Gendo sat in his desk as he went through his paperwork as usual. The Angel's mostly intact corpse was something that SEELE took a great interest in. Even it's S2 organ, while damaged, was still somewhat salvageable. Naturally, Gendo saw an opportunity to increase his funding. ' _I wondered why they didn't take time to properly read the charter for NERV.'_

Much of the charter did come from the former charter that Yui had managed to get from her connections to SEELE. Technically speaking the head of NERV owned the whole organization and any assets that it had or acquired. While SEELE would like to tell him that they were the ones who owned it. It was an empty threat as the wording made it clear that they didn't actually own it. In the end, he did get the increase in funding but he knew that they would want him to do something for them.

Kozo came walking in as he held a report in his hands. The Sub-commander of NERV walked up to his former student. "Well, you might not be liking this."

Gendo took the report and wanted to laugh at it. Apparently, the Japanese government was looking for someone to build an alternative to the Evangelions. It would be insulting if the idea wasn't so funny to read. "They have no idea how to properly even fight the Angels and so they are looking for ways to take back control from me?"

Nevermind SEELE would probably do their best to sabotage the efforts. The next page, however, made him curse under his breath. ' _Son of a bitch,'_ Of course, his father-in-law was doing this to him. ' _He is making me and Shinji come to view it with him.'_

He didn't need SEELE getting their claws into him. If that happens then all his plans would be destroyed. Sure he could try to kill his son but if he did then Yui would likely never forgive him. "You know I think it might be a good idea for both you and your son to have some quality time together for once."

"I will just have Misato and Ritsuko go in our stead," Gendo answered back as he flipped the next page. Then he glared again and slammed his hand on his desk. "If we don't show up our support is revoked?!"

If there was one person he wished to kill with all his might it would be his father-in-law. He just knew he was doing this because he could. Gendo had to hastily figure out a way to keep Shinji under his control. A smirk formed on his face. "Kozo if you could see about getting a marriage certificate."

The elderly man looked at Gendo with a raised eyebrow. Why would he want him to get something like that? "If I may what purpose does that serve?"

Only the best way to ensure that Shinji remained in his control. "Rei has seemed to form a relationship with my son and everything still points to her being obedient to me," Though perhaps he should make a few little changes to this plan on the off chance it backfires. Luckily there was a wild card he could use. "Besides Shinji can consider it his missing birthday gift or some crap."

Kozo just looked at him and wanted to roll his eyes. Just why is it that Shinji had such a terrible father. ' _His mother was also a bit of an egomaniac now that I think about it."_

* * *

Asuka looked at the box that had arrived at the apartment. The redhead could speak Japanese but when it came reading it the girl had no idea how. A fact that made her school work rather hard forcing the teacher to give her homework in English. "They could at least have stayed so I know who to give this box to."

Rei walking up to her looked at the name it was addressed to before taking it out of her hands. "It's mine I ordered it three days ago." Asuka looked as Rei opened the box and pulled out two collars. With something written on both of them. "Hmm, they got the colors mixed up."

"Wait, are those pet collars?" Rei didn't own any pets if she recalled. The only pet in the apartment was Pen Pen so why did she order two pet collars. ' _Wait a minute..'_ Her eyes widened in surprise. "They are for you and Shinji aren't they?"

Rei gave her a nod. After Shinji talked about the adult store she did some research about it as she wondered just what the store sold. Lucky they allowed online ordering and after a quick look, she decided to get something that seemed rather sweet. "The description on the website said that it was for the special someone and came with custom naming for each collar."

There was a small moment if silence as Asuka looked at Rei wondering if she knew just what she had ordered. The answer was very obvious given how Rei seemed to be acting. ' _I wonder how Boy Wonder would react to this.'_ She suddenly pictured both him and Rei with a collar with a leash and both being within her hands. A blush formed on her face for a small moment before she tossed those thoughts out of her head. ' _Why am I thinking about that?!'_

What weird her out more was the fact it was both Rei and Shinji. Asuka was certain that she didn't swing that way. At least she thought she did. ' _Am I bisexual?'_ She thought about that for a second before she turned away and left the room. ' _Why am I asking this it's not like I want to have a relationship with either of them.'_

Rei was about to send her A.T. field in order to found out what was wrong before she stopped herself. Asuka had awakened and with it, her A.T. field was active and trying to figure out what she was feeling could cause her to close herself off. ' _Perhaps mom can talk to her.'_

With Asuka awakened it would be much easier for Lilith to speak to her. Shinji walked into the apartment with a bag of groceries in hand. He looked at the two collars that Rei had. "Did Misato order those for Pen Pen?"

Rei shook her head as she handed Shinji the blue collar. He took it and read the inscription on it. "Property of Shinji Ikari…" He blushed as he saw the name tag on it read Rei Ayanami. "W-w-were did you get t-this?"

Misato walked in with a half-drunk beer can in her hands. She was somewhat drunk. "What's this about me ordering something for Pen Pen?" Misato looked at the two collars for a few moments before taking a sip of her beer. "Are you both thinking of getting a pair of pets?"

"Actually they are for each of us." Rei explained as she held up the collar that had 'Property of Rei Ayanami' written on it. Its tag had Shinji Ikari written into it.

Misato almost dropped the can in her hand at this. The shock almost making her sober. ' _Never took Rei for someone that was into something like that.'_ Misato turned to Shinji as a smirk formed on her face. "You both aren't having fun when we turn in for the night are you?"

* * *

Kaworu walked through the crowds with his hoodie up and sunglasses. Getting to Tokyo-3 wasn't as much of a problem as he thought it would be. Despite their scenario being somewhat altered instead of monitoring him, they seem content with the hands-off approach. ' _I never gave them any reason not to.'_

SEELE was if Kaworu was being honest a bit too single-minded with their goals. Of course, he and his kind also had a rather similar goal looking for Adam in order to remove Lilith's creations from the world. ' _Can't say that we don't understand the irony.'_

* * *

 **You know I've been toying with another story idea. I wonder if I should do it or if someone wants they could ask me about it via pms. Anyway, Lilith has a new ally and it seems that Gendo going to do something that might backfire on him. Does it feel like Lilith has a bit to much of an upper hand? Cause, I think I might need too fix that a bit.**

 **Cya all next chapter.**


	9. Chapter 8

**Another chapter after two days. Oh, boy I've been having a blast writing this. Anyway, time to get on with the show.**

 **Thank you Scattershot98, Hellsink Bathhall, and Reishin Amara for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Asuka awoke from her bed stretching herself before noticing that she was surprisingly naked. She immediately brought her covers up to cover herself as she looked around wondering what had happened to her nightgown she had been wearing. She soon discovered it torn apart along with her new and panties laying at the foot of her bed.

Rei chose that time to make herself known. "If you are wondering last night I saw you tear off your clothes and toss them off before you returned to sleep." Rei herself didn't know why Asuka had clothes for bed. She herself had always slept in the nude. "I choose to make contact with you with my A.T. field and found that the only thought was a bestial desire to remove the outfit that you were wearing."

"Bestial desire?"

Rei gave her a nod before explaining it further. "I believe that it is something from your Angel side effecting you subconsciously," Her mother had told her that there was a possibility of it happening to one of them after an awakening back when she was the only one. "Your fingernails appear to have changed as well."

Asuka brought her hands up noticing that they had sharpened to the point if being almost like claws. Looking at the torn outfit on the floor she could see what she used to cut them. "Sharp teeth and fingernails what's next a tail?"

"That wouldn't be possible as any changes that drastic would have already happened," Rei words caused Asuka to turned to her with a raised eyebrow. Of course, Rei didn't get that it was a joke.

As she looked at Rei a thought crossed her mind of her pulling Rei into her bed. The image of her ripped off her outfit. Asuka shook her head before she screamed at Rei. "Get out of here so I can get dressed!"

Rei took note of the demanding tone but complied. As soon as Rei left the seem Asuka let out a groan. ' _Why am I feeling these feelings!?'_

In the main room, Rei saw that Misato and Pen Pen were already eating breakfast with Shinji. Her plate already prepared for her. Taking her seat Misato looked up from her coffee. "Hey, Rei where is Asuka I thought you were going to get her up?"

"She told me to get out while she got dressed," Rei answered as she took a bite of the eggs. After a few bites, Rei turned to Misato with a questioning look. "Aren't we supposed to have a harmonic test today?"

Misato had a nod as she finished off the rest of her breakfast. One thing Rei had memorized was when she, and now both Shinji and Asuka as well, had tests and training. "Yep and tomorrow you all will have a simulation fight to see how well you can work as a team," Misato looked at both Rei and Shinji with a teasing smirk on her face. "Though I guess the two of you won't be having that much of a problem in that regard."

Shinji had a light blush at this. Misato wasn't ever going to stop teasing him about his and Rei's relationship. Rei for her part seemed outright immune to it. Again that was probably due to her being Rei. "I am certain that the two of us do not require to speak to know each other's plans."

* * *

Rei got her plugsuit on as she felt her mother's presence nearby. The ice blue haired albino pulled herself from her thoughts when she spoke. " _Well, Doctor Akagi now knows most of everything and is on our side,"_ Lilith didn't tell her about everything though. That would come later but right now having one of Gendo inner circle on their side was better than nothing. " _Also, it seems that Gendo is planning to get you and Shinji married."_

That last part didn't make any logical sense to the girl. If she was still under his control won't marrying her off to Shinji only succeed in destroying his scenario? Granted Rei wasn't against the idea of Gendo basically making her desires to be Shinji's mate legal in the eyes of human society. " _You know I feel like I should be worried for you turning into a Yandere,"_ Rei's desire to be with Shinji was starting to reach rather unsettling levels. Lilith was starting to worry if it might be due to her own nature that Rei had inherited. " _Just don't go killing anyone that gets in your way ok."_

The Nephilim had heard the term Yandere before from a few of the Section 2 officers. Something about it being a type of girl in a harem manga. Perhaps she should do some research on this. ' _I think something might be wrong with Asuka.'_

" _Have you asked her what it is?"_ Lilith already suspected that she was growing attached to them both. Inwardly she hoped that this was the case as it meant that the relationship she had hoped would happen.

' _I have not I was wondering if you could talk to her about it.'_ Rei would admit that if she asked Asuka her fellow Nephilim would dismiss her.

Lilith seeing her reasoning pulled back from her. She moved her A.T. field through the headquarters until she found Asuka. The redhead wasn't far from the cages as she was getting ready for her sync test with Eva-2. She was caught up in her focus that she didn't sense Lilith A.T. field touching her own A.T first. " _So you are starting to develop a desire for both Shinji and my daughter."_

Asuka jumped up before realizing that it was Lilith. The redhead cursed under her breath at this. ' _A little warning and for the record, I don't desire them!'_ Asuka tried to deny Lilith but the ancient being wasn't buying it. She did just see her soul after all. ' _I'm pretty sure I don't even like girls!'_

After her fit if denial Lilith if she could, would be rolling her eyes at this. Asuka wasn't denying it out of anything more than fear. Apart of her was afraid of getting close to other people. Especially after what had happened with her mother the last person she had gotten close too. Pulling back from her Lilith moved to Eva-2.

Reaching into it she appeared before the soul of Kyoko. Kyoko awoke from the nap that she had as Eva-2 was being pulled from the LCL. " _Oh, Lilith it's good to see you again."_ Kyoko caught sight of the troubled look on the Angel's face. " _Is something the matter?"_

A sigh escaped Lilith's mouth as she looked at Kyoko. Out of everyone here she was probably the one who could get Asuka to open up. After a moment she figured that it was best to be upfront about this. " _Your daughter desires both mine and Shinji the third Nephilim."_

Kyoko gasped in surprise at this. " _I didn't know my daughter was into that,"_ Come to think of it she wasn't even sure if her child had any interests in anyone else. " _Is this a normal thing for Nephilim?"_

Lilith shrugged her shoulders at this. She made a new species with no idea what she was really doing besides stopping Third Impact. There was a possibility that it was the case or perhaps it was just their own sexuality. " _Whatever the case your daughter is reluctant to attempt a relationship of any kind due to the trauma she suffered when you killed yourself and her doll thinking it was her."_

A wince of pain formed on Kyoko's face at this. Sure her soul was split in two and she was crazy at the time it happened, but just hearing this made her feel like a terrible parent. Lilith placed a hand on her shoulder. " _It's not your fault that happened to you trust me,"_ Lilith showed her the truth of the reason for the accident. Yui was hoping that she would end up absorbed into the Evangelion. Her friend had betrayed her just so she would have a test dummy. " _I am sorry."_

Kyoko felt a great anger well up at this. " _Diese verdammte Schlampe!"_ Kyoko wished she could find and crush her former friend for using her like that. " _Is Yui still around?"_

" _Physically her body is no more while her soul currently rests within Eva-1 currently being piloted by her son,"_ Lilith heard Kyoko curse at her luck. She wanted to get back at her for forcing this fate on her. Lilith could sympathize with her. She still "

had the phantom pains of when her legs were removed. Despite her attempts to heal something was keeping her back. " _Don't worry when this is done I'll make sure to find a way to return you to your daughter while Yui will never leave the tomb she created for herself."_

That was rather comforting to know. Still, that left the issue of her daughter Asuka. The effect her suicide had left on her mind preventing her from having happiness. " _I need to speak to her."_

" _Well, they should be having a harmonic test soon so you can ask her then,"_ Lilith pulled back from the Evangelion as it was set up in the cages with the other Evangelions.

* * *

Asuka took a deep breath as she felt the LCL fluid flood in around her. The blood-like substance was instinctively drunk by her for a moment. Maybe she should ask Rei about why she kept drinking LCL. She crossed that thought out of her mind. The test started to begin as Asuka's synchronization rate continued to climb higher and higher. As it passed seventy Asuka could feel a presence reaching out to her. " _Asuka."_

Her eyes shot wide as the rate started to climb passed sixty. A vague outline formed in the LCL appearing in front of her. The outline touched her head as Asuka suddenly found herself in a dark room as her mother was standing in front of her. Asuka just stared on at her before she finally spoke her eyes widened in disbelief. " _Mama is that you?"_

Kyoko gave her daughter a nod as she pulled her hand back. " _Yes, I've been here within the Eva."_

Tears started to fall out of Asuka's eyes. She thought she was never going to see her again. " _Mama,"_ She jumped to her as Kyoko held her as Asuka let out a lot of repressed sadness. " _W-why did you kill yourself?"_

Kyoko had a pained look on her face. " _Sweetie after I was pulled from the Eva I had half of my soul ripped out of me what you saw,"_ It was mostly a blur yet she knew what her crazy other half had done. Her mental health broken as the metaphysical pain scared her. " _Was effectively a zombie of myself going through the motions until the pain was just too much."_

" _How are you here then?"_ Asuka paused as a realization hit her. Her mother had half of her soul ripped out when piloting the Eva. " _You've been inside the Eva this whole time?"_

A nod answered her question. Asuka knew that the Evangelions were in part living things. Rei confirmed that it was Angel flesh that was used with their creation. " _I believe that each Evangelion is incomplete without one and as such, it takes the first one it can find in this case it took half of my soul before the other half joined it."_

Asuka was starting to have some second thoughts about piloting. The knowledge that she was effectively risking her mother in each battle didn't sit right with her. " _Asuka listen,"_ Kyoko could see that she was thinking of no longer being an Eva pilot. " _I already meet with Lilith and I know the stakes so please don't quit piloting because of me,"_ She had a smile on her face. " _I want to be with you as you face off against Adam's Angels."_

Asuka returned the smile with her own. The thought of fighting with her mother was a nice one. " _Now Asuka do me a favor stop trying to push away your feelings especially for your two other pilots,"_ Asuka was about to deny it but Kyoko raised her hand to stop her. " _Please don't I know you're afraid of letting them in but you can't just push them away because you're afraid."_

The redhead let out a sigh. As much as she wanted to argue she knew that her mother was right. She was trying to push away the desires she was feeling for them. "I-I don't think I can."

" _Then don't think about it and just live in the moment,"_ Kyoko started to fade away as the test was coming to an end. " _Remember I am still here for you."_

With that Asuka found herself back where she was. The outline in the LCL fading away as Asuka looked on. A sigh escaping her mouth as the monitors and computers just looked at the synchronization score sitting at just under one hundred percent.

* * *

Yui looked at her son as his test began before her. She reached out to him taking notice that he didn't seem all that aware of her. A smirk formed on her disembodied face as she took the opportunity to look at what he knew. ' _He is in a relationship with one of my specially made tools?'_

She actually didn't know what she should feel about this. On one hand, she was made that her husband wasn't keeping her out of social contact as she had hoped. On the other hand, she wanted to laugh at how pathetic her son was. His girlfriend being basically a rather advanced doll. ' _... So Lilith isn't inside her after all.'_

Yui figured as much. It turned out that Lilith did use her to create a clone daughter though. A means to stop Third Impact from happening to the world. A reason as to why both him and another girl was altered. ' _What's this he has desires for the girl as well?'_

She wasn't a traditionalist by any stretch of the imagination. Finding out her son was attracted to both a living doll and a foreign girl wasn't her problem. The problem that she did see was the three of them figuring out her plans and goals. As Shinji's sync ratio increases Yui took note if the effects on the S2 organ that was currently growing within her new form. ' _The only reason I will be letting him pilot me is to speed up its development.'_

The organ was critical to her plans. With it, she would have the same power as an Angel. The body she had would officially be an Angel of Lilith. Then the fun would begin assuming the two things she needed for her plans showed up. ' _I will be the one to cause Third Impact on my own terms.'_

As she pulled herself back Yui saw just how tormented his soul actually was. The revelation of being a Nephilim had shaken him greatly. He was divided on either seeing himself as a human or an Angel. Yui finding a means to manipulate him decided to whisper into his mind. ' _You're a freak Shinji and you know it.'_

Shinji blinked as he thought he heard his mother's voice. After a moment he figured it was just his mind playing tricks on him. His sync rank decreased by two points near the end of the test.

* * *

The results of the test were looked over by Ritsuko. Asuka had nearly reached one hundred percent synchronization. The highest out of everyone with Rei coming in second at seventy-seven and Shinji at just around sixty-eight before ending at sixty-six.

Misato looked at the numbers herself almost amazed by Asuka sudden increases. She came with her synchronization rate being sixty and after jumping yo eighty jumped almost to a hundred. "That girl seems to be full of surprises."

' _If only you knew the half of it.'_ Ritsuko had an idea about how Asuka got such a huge score. A combination of Lilith and the soul of her mother helping her. Thinking back to the entity that NERV had imprisoned Ritsuko was starting to wonder just who she could trust within NERV.

Asking Lilith about it was her first thought though to do so she had to go back down to the room they help her. As she explained much of NERV was bugged by Gendo and the MAGI network. The later wasn't a problem to alter for Ritsuko. In fact, she already had done so. The former was more of an issue as Lilith could only tell which rooms had it and not where they were located.

Misato finished a sip of her drink as she looked at the paperwork she had. One of the "joys" of being a captain that she had to look forward too. Looking up from her work she decided to try a little gossip. "You know Ritz Rei ordered both her and Shinji BDSM collars."

* * *

As the three of them walked back to the junkyard that Rei considered the perfect place to train her mind raced with what her mother told her. Looking at both Rei and Shinji though she felt unsure. The both of them appeared to be in a rather strange if happy relationship. ' _Maybe I shouldn't try to put myself into it?'_

Who was to say that she could hold such a relationship? It was just as likely that she ended up destroying it by being apart of it. Asuka pushed those thoughts out of her head. Her mother told her to live in the moment and ignore such things. She'll just have to wait until the right time to confess her feelings and see what happens.

Rei turned to the both of them. The albino Nephilim figured it was time to teach Asuka the next level of A.T. field control. "Asuka in your fight with the Angel you saw it create two energy whips correct?"

Asuka had a nod as she recalled fight with the Angel. She had wondered how it used the energy whips especially given how it didn't have anything to use them like she and Eva-2 had. "Was that something to do with its A.T. field?"

"Correct," Rei closed her eyes as she focused. It had been a long time since she done this. She opened them and pointed at a small pile of trash as her A.T. field solidified. A blast of energy struck the trash blasting it apart. "Besides defending A.T. fields can do a variety of things from the common things like flight to things unique to each Angel."

The both of them looked at what had just happened. They didn't expect that they could do something like that. Asuka was actually excited at the idea of firing blasts from her hands. "So, we all can do that?"

Rei shook her head at that. "No, I have that power while both of you would have a unique ability both with you A.T fields."

That caused Asuka to look at her. Call it bias but she was certain that being able to read minds and blasting energy beams was due to Rei being Lilith's child. Pushing away those thoughts she decided to focus on learning what she could do with her A.T. field. "Alright, so how are we going to find out what I can do?"

"Why you are going to fight me," Rei stated as she got her A.t. field ready to defend herself. Asuka kind of likes this idea. Her wings of light shot out for a moment.

Shinji looking at this decided to get out of the way. He didn't want to get hit by whatever Asuka could do with her powers after all.

* * *

Kaworu could feel that something wasn't right. As soon as he entered into Tokyo-3 he could sense a faint signature of two Angels. Considering there wasn't an evacuation order going out nor was there an Evangelion Unit anywhere to be seen. ' _There is something fishy going on here.'_

The Nephilim of Adam decided to check out the source of what he was feeling. He masked his presence as he headed in the direction of were After half an hour of wondering he came across an old junkyard and while he was there he felt another surprise. "There are three signatures?"

The last one was dormant but there was indeed three Angelic signatures within the junkyard. From the feeling of it, they were not like him. These were not Angels of Adam. As he got closer he got his answer. Sitting on a pile of trash was a boy of his age watching two girls fight.

The first one the redhead seemed to have her wings of light out as she charged her hand covered by an energy field turning into claws. Her attack met the A.T. field of another girl with ice blue hair. "You are starting to get better control over your abilities." Rei stopped as she felt a presence nearby. "Someone is watching us."

Asuka and Shinji were both on high alert at this. Their minds raced for all the possible people that it could be. Section 2 coming to find them. Gendo who somehow caught figured out. Kaworu decided that he couldn't really run away from this. Walking out the Nephilim of Adam made himself known to the Nephilim of Lilith. "I actually thought I was doing a good job at hiding myself you know."

Rei didn't waste any time as her wings shot out and with her hands raised, she fired a blast of energy aimed to kill him. At least she would if he didn't bring up an A.T. field at the last moment in order to block her. Both Asuka and Shinji were stunned to see her try to just randomly attack a guy. Kaworu didn't need to feel emotions to know that the girl in front of him wished to kill him. ' _If I didn't know any better I would almost say that she is Lilith.'_

The difference was subtle but it was there. It was more like she was a direct child or possibly a clone of her. Rei floated back from him literally surprising both of her fellow Nephilim by the act. "Shinji, Asuka he is a Spawn of Adam!" For the first time ever her expression seemed to darken. "He must be killed."

Kaworu looked at the ice blue haired Nephilim who seemed ready to kill him for just existing. With her was two other Nephilim who would also likely jump in and attempt to stab him to death as well. ' _Well, I now know that I am not attracted to females after all.'_

* * *

Lilith could feel hatred coming off her daughter. The connection that she and Rei had was strong enough that she could feel strong emotions from her. Given how that had never happened this caused Lilith to wonder just what could make her stoic child act like this. Reaching out her senses she found an Angel of Adam near them.

Pushing her A.T. field to its furthest she was about to just briefly touch her daughter's and saw what she could see. In front of her was a boy with an A.T. field. Another Nephilim that she knew for a fact wasn't made by her. Anger filled her very being at this. " _Abomination!"_

A Nephilim of Adam. It was a creature fusing the genetics of her creations with Adam. If she could Lilith would personally end this insult to her and humanity. A question arose with this creation. ' _How did it come to be and why didn't the MAGI system pick him up when he used his powers!'_

Rei was ignored by the system and so was Asuka after she did a few minor rewrites to the system. Reaching into the MAGI system she looked through what she could get from the system. ' _I can't seem to access the file,'_ It was there but a more advanced program was keeping her out. ' _How did someone figure out how to manipulate my ships computer systems?'_

* * *

 **Kaworu you done walk into a trap. Also, Asuka begins the trip into turning this into a threeway. Oh, I figured I might try put my other idea as well. So stay tune for another story.**

 **Cya all next time.**


	10. Chapter 9

**Surprise it's not dead! Here is the newest chapter that I've been working on for a while now.**

 **Thank you Scattershot98, emotheextremo, knight7572, Hellsink Bathhall, and TheHiddenLettuce for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Kaworu looked at the three Nephilim before him as he mentally weighed his chances. He was outnumbered three to one. However, from what he could see and guessed the blue haired one was the most trained out of the bunch. The redhead seemed to have just been learning what she could do. The guy seemed unable to do anything. All things considered, he was probably in a much better place than it seemed.

As for the other two Nephilim in question. Asuka after a time to process this barred her teeth out as her A.T. field surrounded her arms with long red claws. If this was one of Adams Angels then she had to take him out. Inwardly a part of her was excited to actually fight an Angel with her own hands. Shinji was the only one that was hesitant. He knew the threat that the Nephilim processed and yes be understand that it was kind of his duty to kill him. The problem was he wasn't seeing an Angel but a person.

That was a problem that both Asuka and Rei didn't have. Rei was more on the Angel side of her existence and Asuka was perfectly accepting what she was. Shinji couldn't get past the fact that in front of him was a guy that looked human even with his strange appearances. ' _It's almost like me.'_

"I take it we can't talk this out?" Kaworu knew that was never happening. Rei was dead set on ending his life. He had nothing against her for it. It was after all her nature to want him dead. "I guess not."

He turned his head over to the pile of garbage next to them and forced his A.T. field out and knocked into it. As it came down Asuka pulled up her A.T. field blocking it while Rei was forced to land and protect Shinji. Kaworu choice that time to race out of there hiding his own A.T. field in the process.

Rei blasted the junk off of her and Shinji as Asuka tore apart the junk with her claws. Rei immediately did a sweep to try to find his A.T. field only to feel nothing. "He has gotten away."

* * *

A chess piece was moved as the recording of an opera played in the background. Before the person was the skyline of Tokyo-2 the current capital of Japan. All around the room was objects both of Japan's past but also important relics from China and even Europe. The sound of a phone call brought their attention as they pulled the phone to them. "Keel what do I owe the pleasure of this call?"

On the other side was the leader of SEELE. The man who had planned much of the events leading up to Second Impact and even today. "If I may ask why are you showing support for the JSSDF attempt to create an alternative to the Evangelions?"

The man had a small laugh as he moved a knight on to its place. There wasn't anyone who seemed to be playing him. No this was all a reflection of his plans and of SEELE's on occasion. "I wanted to see my grandson and well my bastard of a son-in-law just can't seem to let that happen," He took a pawn and set it down on the board. "Don't worry it's not like this will succeed I do expect Gendo to sabotage the whole thing."

Besides, it would allow him to finally liquidate a competitor. Taking a took he placed it opposite of the bishop. While he was all for the plans of SEELE he wasn't one to put all his cards into the plan for immortality. That was why he had built on the legacy of his family. For really to be remembered can be its own form of immortality. "Plus my grandson is one of the pilots and the closest thing I have to an heir nevermind a valuable potential spy."

He took the bishop piece he had and placed it next to the opposing king. With that, the plan was set. The king was tipped over and the metaphorical victory was his. ' _I wonder if Shinji would remember me?'_

"Very, well if you believe this will benefit us then so be it." With that Keel hung up on his side of the phone.

* * *

Rei seemed to be high on alert after the encounter with the Nephilim of Adam. Given he could hide himself from her Rei became concerned on the possibilities that this would cause. Her thought was to talk to Lilith and see if her mother could locate him.

Shinji wondered more on how that was possible for another Nephilim to exist. He did know how both him and Asuka became Nephilim and Rei while vague on her origins, did say that she was made of her mother's flesh. If Adam was against them and the current inhabitants of the planet then how did he come to be? Silently he wondered if it was even possible to stop the fighting.

Asuka was actually slightly disturbed by her own thoughts. Just after the encounter, she began to feel as though she had to stake her claim to her territory. As Rei once called it her _Beastail desires_ wanted her to rip off the offending outfits they wear and claim them. Make them smell of her mark them so that everyone would know that they were hers.

As the three of them wandered back to the apartment Misato's car came racing down the streets and stopping just in front of them. Misato got out of her car as she looked at the three of them with relief on her face. "There you three are I got worried when you three didn't come home."

To be honest Rei and Asuka half expected that there encounter with Kaworu would have set off the MAGI Angel system. Piloting the Evangelions for no real reason on an enemy that was outside of their reach and could hide with the rest of the humans. ' _Strange, only me and Asuka are supposed to be ignored by the MAGI system.'_

If he wasn't picked up by the MAGI system it had to meant that he was ignored by it. Rei knew that only a handful of people could alter the MAGI system too do something like that. Ritsuko and Gendo were out. Given that the former was now allied with them and if Gendo knew about the Nephilim of Adam her mother would as well. ' _Could it be that SEELE was the ones who did it?'_

SEELE was filled with many secrets. Lilith knew only a fraction of what they were doing. Unless either one of them walked into the base, or Two ended up meeting one of them herself, their plans currently were unknown besides their desire for Third Impact.

* * *

Kaworu after having evaded the trio thought about what his next move would be. Finding three Nephilim of Lilith's line was a huge surprise. In fact, he would go as far as to consider it utterly game-changing. The board seemed to have been Adam's spawn vs NERV with SEELE hiding in the shadows ready to destroy everyone.

Now the game was NERV vs Adam's line with both SEELE and Lilith fighting in the shadows. One side hoping to damn humanity, the other hoping to save it through NERV. ' _It looks like that we are not even a big contender in this war.'_

What a cruel joke that is played on his kind. They are looking for Adam in hopes of returning the world to the way they want it. In reality, they are nothing but a tool for an organization that is being used to decide the fate of humanity. If they just disappeared they would be seen as a non-issue. ' _I guess that's the Seed of Knowledge for you.'_

Regardless it isn't like he could save his siblings from attacking NERV. It was very likely that they would ignore him or think of him as an abomination given what he was. Sitting on a nearby bench he contemplated telling NERV about them being Nephilim himself. "No, that would need me to explain how I know that they are Nephilim."

He could see them not believing him if he told them that he was an Angel himself. At best they would grow suspicious of their pilots. At worse they would chalk it up as some kind of Angel trick. ' _Lilith really does hold an advantage.'_

Suddenly an idea crossed his mind. If one or two of Lilith's Nephilim were willing to attack him on sight then that meant that he could probably trick them into revealing themselves. "Look at me already thinking about getting rid of Lilith's chosen."

He guessed SEELE was right. Take away his form and he was still just an Angel of Adam. ' _No, I am Adam trapped in a body that is not my own.'_ That was always so hard to think of himself. There were none of Adam's memories within his mind outside of its knowledge. ' _At the same time, I am not him either.'_

* * *

Asuka hugged the covers over her as she felt extreme annoyance with the thing she was wearing. She had tried going to bed with clothes on hoping she could push away the desire to remove them. So far she was failing as she more she tried to fight it the less sleep she was getting. ' _Fine!'_

Without much fighting, she removed her nightgown and underwear from under the cover of her bed and tossed them to the floor. Asuka let out a sigh of relief as the feeling of annoyance was now gone. She actually felt rather comfortable under the sheets her body as naked as the day she was born. ' _Is this what Rei feels?'_

Her thoughts soon turned to her roommate. How she always slept in the nude. Asuka hands began to move over her body with one of them reaching down as thoughts of her turned to more naught. She started to moan softly as her fingers worked their magic. "Rei… Shinji…"

Her visions slowly got more intense as she pictured both her fellow pilots with her. Her moans increased as did he mumbling of both Rei and Shinji's name. Rei who was somewhat partly awakened by this instinctively sent her A.T. field out to Asuka. On contact, the girl felt bombarded with Asuka desires and her lust above all else. Instinctively she felt her hands moved over herself as Rei copied Asuka motions. The effect only served to feedback into Asuka and then back into her.

Asuka mind started to go blank as she went into a feral bliss. Her teeth nothing into and ripping apart the covers. Rei herself soon joined in as her own instinctive desires demanded she go see Shinji. As she neared her climax a single thought crossed through her mind. ' _Babiesbabiesbabiesbabiesbabiesbabiesbabies!'_

Both girls let out a loud moan at the same time before they laid motionless for a few moments. Rei was the first to move as her fog covered mind. After she left Asuka now on autopilot by her instinct la also left the room in an almost animalistic gaze.

* * *

Shinji awoke feeling himself being held down on both sides by something. At first, he wondered if he was chained before turning to the right and was greeted with the sleeping face of Rei. A blush formed as he looked at her. ' _W-what is she doing in my bed?'_

On the other side, he felt something sharp poking into his shoulder. Turning the other way he was greeted with a mess of red hair that belonged to Asuka who was currently nibbling at his shoulder with her sharp teeth. ' _Asuka too?!'_

He tried to move one his hand only to get a moan out of Rei as he felt himself touching a certain private part of her. In shock, he moved his other hand causing Asuka to moan. His eyes widened in shock at this. Both of them were in his bed and they were both naked. A certain part of him was happy at this turn of events. His mind was, however, panicking at the fact that Misato could walk in and see this.

He tried moving his legs buy both Asuka and Rei had them wrapped around theirs and kept him from moving. It was as if they had both wakes into bed and wanted him to stay down until they woke up. Luckily for him, both of the girls started to stir. Rei was the first one to awake of the two and in her half sleep state brought herself up to Shinji's face. She kissed him as her mind was still somewhat within her dreams of them being married. "Morning."

Her kiss was soon joined by Asuka sucking on his neck before licking it with her tongue. She spoke softly in her mother tongue. "Meine liebe."

It only afterwards did both girls become aware of each other's presence. Asuka and Rei stared at each other while Shinji could just fill the awkward silence in the air around him. The two girls stared at each other before Rei spoke. "Asuka what are you doing in bed with me and Shinji?" She then paused before realizing what she just said. ' _I am also in Shinji's bed with him…'_ While Rei didn't react visibly a blush did form on her face. "Wait did you just say _my love_ to Shinji?"

' _That's what she said?!'_ Shinji's train of thought ended with him taking notice that Rei was glaring at Asuka.

Rei continued to stare at Asuka as the redhead thought she could see an air of terror around her. This wasn't how she pictured any of this happening. Suddenly the feeling of terror disappeared. "I get the first baby."

Silence filled the room yet again at this. Asuka blinked as she made sure she had heard that right. "What?!"

"You can be with Shinji as well but I will be the one having the first baby with him," Rei stated like it was a fact. Shinji for his part wondered when Asuka had fallen for him and why Rei was treating him like he was her possession.

Asuka wanted to blow it off or anything. However, instead of what she would usually say she didn't feel herself wanting to do anything but accept. "I wasn't planning on having kids for a while anyway."

Shinji finally chose that time to speak up. "Did you both just agree to share me?"

"I think so," Asuka answered as Rei simply gave him a nod.

Shinji should feel mad about this. He wasn't an object after all. Though he wasn't protesting this like he should. In fact, the idea of being with the two girls was rather appealing. Suddenly his door opened up as Misato walked in, "Shinji do you know where…" She stopped as she saw him in bed with the two girls. "Please tell me you used protection."

* * *

" _So, let me get this straight you couldn't find the Nephilim of Adam at all?"_ Rei gave her mother a nod as she waited for her check up to finish. Ritsuko had offered to just put it into the system that Rei had been here for it. After all her body was perfectly stable thanks to her mother alterations.

She chose against it only because Gendo had secret recording devices throughout the room in question. Rei had to go through it just to keep up appearances. ' _Unfortunately, it appears he has learned how to hide his A.T. field.'_

This was not what Lilith wanted to hear. On the bright side due to his status as a Nephilim, he couldn't cause Third Impact for Adam's kind. His form was an abomination both to them and to her. Her thoughts were transmitted to her daughter who had thought about it as well. " _Now, you and Asuka are sharing Shinji?"_

Rei gave another nod. ' _Yes, but I have made it clear that as his first mate I get the right to his first baby,'_ While she won't say that Asuka might attempt to take the first child from her Rei had made it clear that she was Shinji's first. A giggle came over Lilith at this. ' _What is it?'_

" _Dear, Asuka has feelings for both Shinji and you."_ Lilith's words caused Rei to show some surprise. Asuka having feelings for her was indeed surprising.

Rei thought about it for a few moments. Asuka was rather attractive if Rei thought about it. Especially when she was in her plugsuit. There was a slight shudder as Rei hands almost shot down between her legs. ' _If she wants to be mates with me as well then I accept.'_

Lilith was happy to hear this. At last the triad relationship between then was coming true. She couldn't wait to talk to Kyoko about this. Lilith slightly wondered if she would be ok with being called grandma from a bunch of Shinji and Rei babies. ' _You hoped for us to get together?'_

Right the connection was still going on. Lilith for her part had an awkward laugh at this. " _Well, yeah I mean you got to admit you three are a new species and I want you each to be happy so being together made a lot of sense."_

Rei could understand that. The LCL around her was soon flooded away as Ritsuko stopped the checkup. As soon as Rei walked out she sent her A.T. field out to Ritsuko. The head scientist of NERV had gotten rather good at noting when Rei or Lilith was making contact with her. ' _You know you don't have to talk to me like this.'_

' _It's better to not leave anything to chance.'_ Rei took the tool that she was given to dry off some of the fluid off. The daughter of Lilith had grown used to this routine anyway. Sure once everything was done and Gendo and SEELE were defeated she couldn't do this anymore. That did bring a slight frown to her face as she had come to enjoy the time. ' _Also, I should warn you that yesterday we encounter another Nephilim though this one was of Adam.'_

Ritsuko hid her shock as well as she could at this. Adam had a Nephilim of his own? ' _How is that possible I thought the three of you were only possible because of Lilith.'_

Rei had no idea how that was possible either. Adam wasn't the one who caused it that was for sure. The current idea that Rei was going with was that he was like the bunch of Rei's currently in storage. ' _Perhaps he is a clone made with a mix of human and Adam's DNA.'_

At the word of clone, Ritsuko thought back to the large tank with numerous clones of Rei. Ritsuko wondered what she should do about those soulless shells. Gendo was making another one for a dummy plug system. Why he didn't want to use the others was simple. He wanted to use younger more malleable minds to make his planned system easier. Ritsuko wondered if she could possibly sabotage the system while Gendo was away. ' _If he ever got away from the base.'_

No sooner as she thought about that did she and Rei find Gendo standing in front of them both. The Commander of NERV stared at Rei unaware that the ice blue-haired girl had already taken a look at what he was thinking. ' _He has a marriage certificate for me and Shinji to sign,'_ She wanted to blast him for his more darker thoughts. ' _Using the fact Yui's DNA was used in my creation to break him.'_

Rei knew that she wasn't his sister. The mutations between the both of them took care of that. Rei made note to tell him about her origins as soon as possible in order to undermine his efforts. "Doctor Akagi I would like to speak with Rei for a few moments."

Ritsuko turned to Rei before walking away. Gendo looked at the girl as Rei continued her obedient little doll routine while in front of him. "I want you to marry my son."

' _I was already planning to.'_ Perhaps she could use this as a means to make it official early. "Is there anything else?"

* * *

Shinji and Asuka both looked at Rei as they looked at her with wide eyes. Rei had told them of Gendo's plan to get her and Shinji married. "So my father wants us to get married?" The man who Shinji knew couldn't care less about him wanted him to marry Rei. "Why is he doing this?"

"Because he hopes to break you with the truth of my origins," Asuka and Shinji turned to her as Rei knew what they were thinking. The fact that she was part Angel. Yet, that wasn't the secret she was talking about. "As you both know Lilith's DNA is used in my creation it along with my soul makes me the daughter of Lilith but half my genetic makeup is from another source."

The both of them hadn't asked about that. Though seeing what Nephilim were they had to figure that Rei had to have another genetic source. "So what is it why does my father think it would break me?"

There was hesitation from Rei. She was afraid of what would happen if she opened her mouth and told Shinji as to what happened. For a moment she felt her mother's A.T. field brush against hers. "It's from them that I got not just my DNA from but also my last name and my appearance," Rei looked at Shinji for a moment before letting out a sigh. "Yui Ikari is the source of the human DNA used to make me."

A pin could drop and it would be heard echoing through the room. Rei wanted to look away as the other two Nephilim just stared at her. Asuka finally broke the silence. "You're made from his mother?"

Shinji couldn't believe what he was hearing. Rei was made using his mother's DNA. That meant that they were related. "Y-you're my s-sister."

Rei gaze hardened at this. "No, I am not," Her tone of voice cause the both of them to stop and looked at her. "When Yui used her DNA to make me it suffered numerous mutations when introduced to my mother's," She motioned to her hair and eyes. "By the end of it much of her original DNA was so heavily altered that the only thing that exists as proof of our connection is my appearance which she purposely molded in her image."

"So, you aren't his sister but you look like his mother," Asuka tried to understand what she was getting at. She was suddenly creeped out at the thought of someone making a person after their own image. Rei gave a nod in confirmation.

Shinji himself didn't know how to feel. While he was relieved that it wasn't the case he still had a question. Why did his mother make someone in her image? ' _Was my mother a narcissist?'_ He'll look into this later. "I can see why you would want to keep this a secret," Suddenly a thought crossed his mind. "Wait does that mean I am not related to my father?"

* * *

Mari looked out as Unit-4 was loaded up into the aircraft carrier. No sooner as it was finished did she learn about her new assignment. She was to be flown to NERV's headquarters to work with the other three pilots. ' _The First, Second, and Third child.'_

She looked at the folders given to her and looked at each of their appearances and profiles. Both Rei and Shinji didn't look like they were normal and at first glance, Asuka did until she noticed the cat-like appearance of her eyes. ' _She had teeth that are razor sharp?'_

Something was off about this. She wondered if she could call _him_ and see if he knew the reason. He did know about SEELE and what happened to her mother after all.

* * *

 **Five days until Christmas. I don't know if I would have a chapter out or take the day for myself. Whatever the case I am happy to report that this story is not dead. I figured a few of you thought of that. Oh, and the triad is finally formed. Ten chapters in including the prologue.**


	11. Chapter 10

**I have returned one more time before the new year! It looks like I am closing out this year with Evangelion.**

 **Thank you c0l0r-bl1nd n355, Scattershot98, Hellsink Bathhall, and Dragonjek for your feedback, thoughts, and questions. I also like to thank the readers along with those that favorited and/or followed the story.**

 **Disclaimer: Neon Genesis Evangelion and Rebuild of Evangelion are the property of Gainix, Studio Khara and Hideaki Anno. I own nothing and please support the official release.**

* * *

Shinji's question on his relations with his father caused a brief moment of silence between everyone. Rei gave him a nod in confirmation. "As your body developed into a Nephilim your genetic code was rewritten with the remaining human genetics being suffered to mutations as of now you likely share at most five to eight percent of your genetic code with Gendo," It was around the same with Yui as well but Shinji had not asked that of her. "Of the three of us, Asuka is the least mutated and shares around thirty-five percent of her genetics with her mother."

After hearing this Shinji felt relieved. He really didn't like his father and this latest action just destroyed what little bit him that still wanted his approval or really anything. Hearing that he wasn't, genetically speaking, his son felt like a weight lifted off his shoulders. Now there was just the issue of Gendo attempt to force a marriage on both him and Rei. "So, what are we going to do about the fact he wants us to get married then?"

"We get married," Rei simply stated it as both Asuka and Shinji waited for her to continue. After almost a full minute of waited for her to add anything to it. "That's it."

Asuka rolled her eyes at this. Of course, there was no plan besides her getting her husband of choice. "You're just going through with it because you want to be his wife."

"I do not deny that," Rei answered causing a blush to form on Shinji's face. Inwardly he wondered why this had happened to him. Not that he was complaining but it felt like this was way to fast. "Yet, there is one twist we could do to it."

Before Asuka or Shinji could ask Rei brought the redhead into a kiss. Asuka's eyes widened surprised before she returned the kiss even before her mind realized what was going on.

* * *

Gendo stared at Rei and then at both Shinji and Asuka. He had ordered Rei to get his son to marry her, and surprisingly he was onboard with it very quickly. The one problem was that somehow they both had a relationship with the Second Child as well and thought it was only fitting that they all get married together. He was almost certain that Kozo was mentally laughing at him for not knowing this.

Unknown to him Lilith was laughing at him. The man was caught with his own attempt at breaking his son being thrown into chaos. Taking a look at his feelings she saw the conflict as he wanted to call this off. He knew if he did the Asuka and Shinji would get suspicious. "Very well then," He pulled out the paperwork that he had for this. "I have a judge approve it and you three can have the ceremony later."

Gendo fought back his annoyance as he watched the three of them sign. Rei and Shinji in Japanese while Asuka just wrote her name in her native language. After that, he dismissed them both as he looked at the signatures. " _Rei Soryu, Shinji Soryu…'_ They were using Asuka's last name. Not his and not Yui's maiden name, which Rei had been using. ' _If I didn't know any better I think they did this just to spite me.'_

Without a word, he handed it to Kozo. The Sub-Commander looked at him as he took the papers. He didn't say a word as he watched Gendo leave the office. ' _Something didn't go as you had planned it seems,'_ If he was being honest he felt like congratulating the newlyweds. Even if Gendo had attempted to manipulate them together in an attempt to destroy his son. ' _Now then who would be willing to perform a three-way wedding ceremony?'_

Lilith's retreated her A.T. field from the room and pulled it to Rei. She could feel a well of joy just waiting to burst from her. The daughter of Lilith just got what she had been wanting for a while now. Plus, she just screwed Gendo plans without making any indication that she wasn't what she thought he was. " _Rei Soryu?"_

' _It was my idea actually,'_ Shinji didn't want to have his father's last name anymore. At first, he had wanted to take Rei's but she knew better. After all, she didn't like her last name either for reasons known to her and Lilith. By process of elimination that just left Asuka's. ' _Plus, The Commander didn't seem to like it.'_

Rei heard a laugh from her mother at this. She did a little probe with A.T. field and saw that Gendo was going to Eva-1. With a touch on his A.T. field, she saw that he was planning to tell his wife about this. ' _Is it sad that he has no idea how little she cares about him?'_ Speaking of parents, she should tell Kyoko about this.

* * *

Misato blinked as she read the names on the three new ID cards Kozo gave her. NERV updated theirs every six months and as the current guardian to the three pilots, she was tasked with giving them to the children. The three current ones seemed to have an error as they each had Asuka's last name on each of them. "There an error Shinji's should say Shinji Ikari and Rei's, Rei Ayanami."

"I assure you there is no mistake," It was a last minute change to be sure. Knowing how new it was Kozo decided to explain. "The three children are now married and decided on Asuka's last name."

A laugh escaped Misato's mouth at this. When she was done she handed him back both of the ID Cards. Kozo looked at her with a serious expression feeling kind of insulted that she would think he was joking. "This isn't a joke?" She paused before shooting up from her desk. "What the hell they are only fourteen!"

Misato winder who would do such a thing like this. Sure, the laws for marriage were still technically laxed after Second Impact but letting them decide to get married? It just sounded like a mistake waiting to happen. "Yes, but given the line of work they had the Commander thought it was best just in case things ended badly from them, have no regrets if you will."

She couldn't believe what she was hearing. The Commander was the one who allowed this. Misato sat back down in her chair. ' _Great, let a bunch of teenagers get married while they are piloting join robots.'_ When they got home she was going to have a serious talk with all three of them. "Is there anything else I should know?"

"Yes, we want you to be the minister for the ceremony, you are officially licensed if I recalled." Kozo had a smirk as Misato groaned as she recalled that. She had gotten drunk one day in college and took on a dare which ended up with her being ordained as a minister.

It was one of several things she had foolishly done and the only one that she couldn't cancel or get rid of. Still, she had reservations with marrying the children. "What if I refuse?"

Now it was Kozo turn to have a chuckle. He pulled out the employee rule book. "While I can't order you too, however, The Commander is having it become something of an official company party and according to the rule book if you are ordered to attend you will attend barring important commitments," It said something to Misato to learn that Gendo was forcing her to marry the children by making it a party. "As you can guess you are ordered to attend and perform the ceremony."

' _Is he trying to be an asshole?'_ What was she saying of course he was. It was clear to most of them how much of a jerk their Commander could be. Especially, given how he acted to his son and Rei.

* * *

Within Eva-1 Yui didn't know what to feel about what Gendo had told her. Her son had gotten married to one of the little dolls she had made and the daughter of Kyoko. For a moment she wondered if she should laugh at him or at Gendo. ' _Like I care that what he decides is his type.'_

For Gendo Yui knew that he was being manipulated. Not by SEELE like he expected but by _her_. The thing that he thought was effectively broken beneath them. ' _Lilith is playing you like a fiddle and you don't even know it.'_

Speaking of Lilith, in Eva-2 the ancient being was informing the good news to Kyoko. She, of course, was happy for her daughter though she was also extremely worried. "I know that Gendo kind of forced their hand but really with the rate they are going I fear Asuka might end up as a teenage mother."

Lilith didn't question about what was so bad about it. Sure, She could understand Kyoko's worry given how old and the kind of life Asuka had. The thing is she knew that both Rei and Asuka were sexually mature in the biological sense and that Rei was likely to jump at the first chance they had to become a mother. "I won't worry too much about it Rei made it very clear that she's going to be the one who has the first baby and Asuka's not ready yet for her own."

"Aren't you worried all that worried about Rei?" Kyoko figured it was due to Lilith being what she was.

Lilith already knew that Rei was going to wait until the war with Adam's kind was over. When both SEELE and Gendo were defeated her little girl would be free to live her life with her two mates. As soon as that was done then she would start having kids. "My daughter inherited my drive to create life and I admit I can't wait to hold my little grandchildren," There was a giggle at this. "I think I might be the only one of my kind who gets to claim she has grandbabies."

At Lilith's words, Kyoko couldn't help but feel sad. Her old body was gone having been killed by the fragment of her soul that had been driven mad. It was impossible for her to leave Eva-2. Lilith put a hand on her shoulder. "I know you think you are trapped but that won't be the case forever I am sure I can help you find a way out so that you too can be with our family again."

* * *

Rei had been rather adamant that she and Asuka move into Shinji's room when they got back to the apartment. While Asuka and Shinji figured that they would be using the marriage as a means to prevent Gendo from having what he wanted Rei didn't. Yes, it was part of that but Rei wanted them to take this seriously. "I don't think we'll be able to fit all the beds together in the room."

Shinji's room was only just barely bigger than Asuka and Rei's room. The two beds, well a bed and a mattress on boxes, in their room barely left them with any space as was. Rei turned to him as she put her clothes down. "We'll only need a single bed to sleep in for the three of us."

The simplicity of which she said it brought a blush not only on Shinji's face but also to Asuka. The boy couldn't help with picturing the two girls on his side's naked like when he woke up earlier today. Asuka for her part felt a desire to take the both of them into the bed right now and lay her claim to them. She tried to push this out of her mind but she couldn't. Her instincts didn't want to be denied.

"Ar-are you sure?" Not even a day and already he was being submissive. He wondered what was wrong with him? ' _I just got married to two beautiful girls.'_

Legally at least as the ceremony hadn't been performed but as of now, he was Shinji Soryu. The thought of it did feel uplifting. "Rei, Shinji, Asuka!" Misato's voice yelled through the building as the three of them saw their guardian looking at them with her arms crossed. "You three wouldn't mind if we had a talked?"

Half an hour later Misato had drunk three beers as she listened to the three of them explain why they had gotten married. The story they both had gone with was that they didn't know how long they would live given the kind of life they had. Rei stated quite only answering when she was talked too. She was debating if now was as good a time as any to tell Misato about the truth of their existence. Reaching out with her A.T. field she could feel her thoughts about this. ' _She being forced to perform the ceremony.'_

There was also some sadness and even a bit of her wondering if she'll ever get married. Misato was jealous of the fact the two of them found someone. Pushing further she saw Misato's hatred of the Angels. Caused by Second Impact when Adam had awakened and the resulting fallout. Rei stood up and walked to Misato. "There is something more that I think you should know."

This was something she had never done before. Theoretically, any Angel, Adamian or Lilithian, could do something like this. Placing her hand on Misato's shoulder her A.T. field reached into her as she undid the damage that being near Adam's awaking had caused her. When it was done Misato was greeted with Rei revealing her wings of light.

* * *

It took a long time to get Misato to calm down after seeing Rei reveal her nature to her. Once that was done Rei, Asuka, and Shinji each could see her looking at the three of them. She was very close to having a nervous breakdown as she looked at the three of them. "You mean to tell me that the three of you are part Angels, that NERV is built inside of a ship used by the Angel within the basement, and the Evangelions are actually…" She couldn't bring herself to answer that. "What the hell is NERV actually fighting for?!"

"The leadership of NERV are fighting to cause Third Impact on their terms," Rei's answer made her want to drink even more. Misato felt like she had been used. "They just need to get Adam's Spawn out of the way before they attempt it."

Misato didn't know how but she felt like she had to tell everyone the truth. NERV was effectively a threat to everyone using the pretense of helping. She gripped her beer can crushing it. "What about you what does Lilith want out if this?"

She couldn't see Rei the same anymore. The girl was the daughter of the Angel that NERV had. One of the things she hated. One of the things they should destroy. Hypocrisy seemed to be NERV's thing given they used Angel flesh to create the Evangelions. Even Shinji was surprised to hear this and he was one of them! "Lilith wants to stop it," Rei figured it was easier to show her why. Touching her A.T. field Rei feed the information of Lilith's connection to the current life on earth. ' _Everything on this world his hers and she doesn't want it to end either by Adams' hand or by anyone else's.'_

That just about completely changed her worldview. The source of all life on earth was an Angel. The one that caused Second Impact was her opposite and right now there were three sides in a war. NERV, Adam, and Lilith. "Does anyone else know about this or am I the only one outside of you three?"

"Doctor Akagi knows the truth," Misato wasn't surprised. Ritsuko was practically wanting to adopt Rei with the way she acted. For a moment she wondered if she could tease her about wanting to be in a relationship with an alien.

Misato took another drink of her bear as she paused. By know, she should be feeling something. Even with her high tolerance. "I took the liberty of healing the effects that Second Impact had on your body," Rei paused as she looked at the bear. "I may have also made it impossible for you to get drunk as an unintentional side effect."

Shinji was ok with that while Asuka held back a desire to laugh. Misato tossed the now empty beer can to the side. Great now that was taken from her. "Wait," She turned to Rei making sure she heard that right. "As in everything including…"

Rei had a nod as Misato almost immediately moved her hand to her stomach. Her eyes widened in surprise before she shot up in joy. That was now finally an option for her to be a mother. "Thank you!"

"What exactly did you do?" Asuka asked the blue-haired girl.

"I managed to fix the biological damages that being next to Adam when he caused Second Impact," Rei answered treating her action as mostly a non-issue. Both Asuka and Shinji looked on surprised that she could even do that. "I will teach you both how to do it when you each have better control over your abilities."

"We can heal people?" Shinji questioned surprised by that.

Rei gave a nod as while his assessment was correct it was far more complicated than simple healing. Misato next to her groaned as it was as Rei said by now she should feel something but another can and nothing was happening. "You shouldn't try to get yourself drunk you can still suffer alcohol poisoning."

Misato just groaned before she tossed the partly drunk beer can into the ground. She didn't even bother with the fact it was dripping the alcoholic substance on the ground. "I could have your mind simulate the sensation," Misato turned to the girl who both healed her and removed her ability to be drunk with a nod.

* * *

Shinji sighed slipping into bed. In the end, it seemed that Misato was onboard with the whole stopping Third Impact. He thought about all that Rei had explained. Knowing what his former father had planned for the world made him hate him even more. How that was even possible at this point spoke volumes about the kind of man that he was.

His mind paused as he remembered what Rei told him about her origins. Made by his mother using her DNA with Rei's appearance modeled after her own. Then there were those memories. The first one with her laughing wickedly and the other. ' _She drugged me.'_

A horrifying thought crossed his mind. What if his mother was as worse as his father or more so? Shinji shook his head as he pushed those thoughts away. Sure, his mother may have done some questionable things but she was still the kind woman he knew her to be. ' _Right?'_

Shinji was pulled out of his thoughts as Rei entered the room without any clothes besides her towel. Shinji's eye shot open at this before he tried to look away. This was soon impossible as Rei enter into the bed and kissed him. "Why are you wearing clothes?"

"Wh-why aren't you?" Shinji fought back the little voice within his head that told him to not question it.

Rei gave him a questioning look. She had done a bit of reading beforehand and it seemed like Shinji had no idea. "It's customary for a married couple to consummate their marriage on the night that they got married," She was certain she had gotten that right. "Is there something wrong?"

He tried to find words but all that come out was nothing. The door opened up as Asuka walked in with a towel covering herself. She looked at the two of them in bed. "You work fast don't you Wondergirl," Looking at the both of them Asuka could feel the beast within her hunger. "Move aside."

Before Shinji know it Asuka tossed her towel down and joined Rei and him in bed. He tried to do something about this but finally, he couldn't hold back the voice in his head anymore. More than an hour later in the nearby room, Misato in a simulated drunk state thought she could hear something coming from the newly married couples room.

* * *

Shinji awoke to the feeling of being a bit worn out. He immediately noticed that Asuka was nibbling on his neck opposite to the side that she had bitten. A shiver when down his spine. Halfway through it, Asuka went, as Rei had called it, feral and started clawing and biting the both of them. ' _Is it wrong that I was turned on by that?'_

Small bits of pain lingered from were Asuka had clawed at him with her nails. The girl had made sure to keep him down as she marked him. Turning to the side he saw Rei sleeping peacefully with a scare of her own on her neck from were Asuka bit her. ' _Why do I hear purring?'_ Turning to the redhead girl laying on top of him he got his answer. ' _Asuka purs.'_

If he didn't know any better if she had cat ears and tail it would be almost fitting for her. Maybe that was what she would look like as a full Angel. Some kind of feline. Just like that, his mind formed a picture of a catgirl Asuka looking at him seductively. Shinji was removed from his thoughts when Rei brought him into a morning kiss. "Morning."

As she did Asuka woke up with a stretch giving both of them a full view. She blinked for a moment before noticing am the scratch marks on both Rei and Shinji. "Did I do that?"

"You did," Shinji had a blush as he remembered feral Asuka and the kind of wild loving she gave both him and Rei.

Rei looking at her marks she didn't see anything wrong with them. She knew the reason that Asuka had done it even when feral. "She was just marking her territory making her claim to us known."

A blush formed on Asuka's face. She had been fighting back her desires to claim them for a whole day and when she did she not and clawed at them. Like, some wild beast that was taking a section of forest for herself. In this case, it was her making it clear to any potential 'rivals' that they were hers. "Th-this won't happen again."

"I kind of like it," Feral Asuka actions played in his mind. He didn't like being a scratching post but he couldn't deny he enjoyed it when she went wild.

"I agree with our husband," Rei pulled Asuka close. "It was caught an experience." Their lips met as Asuka and Rei kissed right in front of Shinji.

Looking at the turn of them a small smile formed on his face. If this was his future then he could get used to it. ' _I guess there is something to look forward to when It's all over.'_

* * *

It's first thought was to locate anyone else of its kind. So it floated along the water sending signals all around to locate one of them. In the end, none could be found. Instead, it decided to head for the signal. Perhaps it could find the one who spawned it and helped it remake the world to the way it wanted. As it floated over the sea it saw the creations of them.

The current inhabitants of this world. Those that came into being from another progenitor. Its body moved and opened into strange shapes before firing a laser into the shipping vessels. In one shot a company lost millions while the crew lost their lives.

As it returned to a floating octahedron it heard a voice echoing in in its mind. A fellow creation was swimming through the sea underneath it. It had just grown to adulthood and sadly couldn't help it. After a brief exchange, it agreed to wait in the sea and see it it could harass these creatures ships. With that, the geometrical Angel floated on leaving its brother to its newly appointed task.

Several hundred miles from it the U.N. fleet moved unaware of the threat lurking under the waves.

* * *

 **Two angels attacking two different targets. The next chapters are going to be a huge pain to write when the time comes. I am going to love it in the end. As that is just me.**

 **Cya all next time. Have a happy New Year.**


End file.
